Starting phenix.real_space_refine on Thu Feb 22 00:49:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x74_33031/02_2024/7x74_33031.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x74_33031/02_2024/7x74_33031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x74_33031/02_2024/7x74_33031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x74_33031/02_2024/7x74_33031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x74_33031/02_2024/7x74_33031.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x74_33031/02_2024/7x74_33031.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 14 6.06 5 P 172 5.49 5 Mg 1 5.21 5 S 112 5.16 5 C 19811 2.51 5 N 5834 2.21 5 O 6606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 11": "OE1" <-> "OE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 76": "OE1" <-> "OE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C GLU 278": "OE1" <-> "OE2" Residue "C GLU 452": "OE1" <-> "OE2" Residue "C GLU 476": "OE1" <-> "OE2" Residue "C GLU 553": "OE1" <-> "OE2" Residue "C GLU 678": "OE1" <-> "OE2" Residue "C GLU 684": "OE1" <-> "OE2" Residue "C GLU 781": "OE1" <-> "OE2" Residue "C GLU 803": "OE1" <-> "OE2" Residue "C GLU 804": "OE1" <-> "OE2" Residue "C GLU 829": "OE1" <-> "OE2" Residue "C GLU 846": "OE1" <-> "OE2" Residue "C GLU 894": "OE1" <-> "OE2" Residue "C GLU 937": "OE1" <-> "OE2" Residue "C GLU 1002": "OE1" <-> "OE2" Residue "C GLU 1006": "OE1" <-> "OE2" Residue "C GLU 1095": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D GLU 489": "OE1" <-> "OE2" Residue "D GLU 493": "OE1" <-> "OE2" Residue "D GLU 550": "OE1" <-> "OE2" Residue "D GLU 674": "OE1" <-> "OE2" Residue "D GLU 952": "OE1" <-> "OE2" Residue "D GLU 1028": "OE1" <-> "OE2" Residue "E GLU 74": "OE1" <-> "OE2" Residue "F GLU 385": "OE1" <-> "OE2" Residue "F GLU 412": "OE1" <-> "OE2" Residue "F GLU 426": "OE1" <-> "OE2" Residue "F TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32550 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1742 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 13, 'TRANS': 212} Chain: "B" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1792 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 13, 'TRANS': 219} Chain: "C" Number of atoms: 8692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8692 Classifications: {'peptide': 1116} Link IDs: {'PTRANS': 58, 'TRANS': 1057} Chain: "D" Number of atoms: 9846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1259, 9846 Classifications: {'peptide': 1259} Link IDs: {'PTRANS': 56, 'TRANS': 1202} Chain: "E" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 597 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "F" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2379 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 285} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "M" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "N" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "O" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1714 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "P" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1729 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "Q" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 108 Classifications: {'RNA': 5} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12673 SG CYS D 60 79.405 105.081 115.600 1.00 89.92 S ATOM 12691 SG CYS D 62 78.425 106.446 118.672 1.00 92.64 S ATOM 12800 SG CYS D 75 81.725 105.107 118.292 1.00 92.95 S ATOM 12826 SG CYS D 78 79.543 102.402 118.777 1.00 89.64 S ATOM 19225 SG CYS D 886 108.319 51.187 83.854 1.00 89.23 S ATOM 19789 SG CYS D 962 105.034 51.322 85.140 1.00 75.30 S ATOM 19837 SG CYS D 969 105.603 53.110 81.641 1.00 66.75 S ATOM 19856 SG CYS D 972 105.394 49.445 81.961 1.00 74.56 S ATOM 25704 SG CYS G 90 86.606 185.316 86.727 1.00190.55 S ATOM 25726 SG CYS G 93 84.097 187.108 84.454 1.00191.16 S ATOM 25999 SG CYS G 130 85.156 188.165 88.144 1.00181.18 S ATOM 26018 SG CYS G 133 82.623 185.515 87.499 1.00174.23 S ATOM 25618 SG CYS G 79 102.355 191.689 83.182 1.00192.00 S ATOM 26688 SG CYS H 90 116.446 168.898 96.542 1.00190.67 S ATOM 26710 SG CYS H 93 118.318 166.112 98.232 1.00190.26 S ATOM 26983 SG CYS H 130 118.500 169.682 99.670 1.00187.29 S ATOM 27002 SG CYS H 133 120.323 168.508 96.384 1.00182.07 S ATOM 26602 SG CYS H 79 101.099 167.249 103.859 1.00179.93 S ATOM 27672 SG CYS M 90 83.012 176.677 42.752 1.00186.96 S ATOM 27694 SG CYS M 93 79.996 177.992 44.807 1.00185.83 S ATOM 27967 SG CYS M 130 79.557 176.422 41.337 1.00187.59 S ATOM 27986 SG CYS M 133 81.166 179.882 41.828 1.00182.16 S ATOM 27586 SG CYS M 79 82.168 161.855 47.847 1.00184.71 S ATOM 28656 SG CYS N 90 106.872 152.110 37.598 1.00184.39 S ATOM 28678 SG CYS N 93 110.500 150.877 37.218 1.00182.76 S ATOM 28951 SG CYS N 130 107.828 150.174 34.553 1.00182.02 S ATOM 28970 SG CYS N 133 107.755 148.369 37.846 1.00175.03 S ATOM 28570 SG CYS N 79 106.598 164.781 28.454 1.00186.86 S Time building chain proxies: 17.18, per 1000 atoms: 0.53 Number of scatterers: 32550 At special positions: 0 Unit cell: (147.4, 220, 200.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 14 29.99 S 112 16.00 P 172 15.00 Mg 1 11.99 O 6606 8.00 N 5834 7.00 C 19811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.60 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb=" ZN D1403 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 972 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 969 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 886 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 962 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 130 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 90 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 93 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 133 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" NE2 HIS G 85 " pdb="ZN ZN G 202 " - pdb=" NE2 HIS G 87 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 79 " pdb=" ZN G 203 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 122 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 86 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 84 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 93 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 90 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 133 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 130 " pdb=" ZN H 202 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS H 85 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS H 87 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 79 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 86 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 84 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 122 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 133 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 130 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 93 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 90 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 79 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 85 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 87 " pdb=" ZN M 203 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 122 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 84 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 86 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 130 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 133 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 93 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 90 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 79 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 85 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 87 " pdb=" ZN N 203 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 86 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 122 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 84 " Number of angles added : 36 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6876 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 48 sheets defined 44.1% alpha, 13.3% beta 68 base pairs and 116 stacking pairs defined. Time for finding SS restraints: 12.38 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 82 removed outlier: 4.273A pdb=" N GLN A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 203 through 225 removed outlier: 4.166A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.757A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 83 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 203 through 221 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.829A pdb=" N THR C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 221 through 229 removed outlier: 3.905A pdb=" N LEU C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 241 Processing helix chain 'C' and resid 243 through 253 Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 276 through 289 Processing helix chain 'C' and resid 297 through 309 removed outlier: 3.716A pdb=" N LYS C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 337 removed outlier: 3.595A pdb=" N GLY C 337 " --> pdb=" O LYS C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 366 through 392 Processing helix chain 'C' and resid 399 through 404 removed outlier: 3.738A pdb=" N ILE C 404 " --> pdb=" O PRO C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 418 removed outlier: 3.524A pdb=" N VAL C 410 " --> pdb=" O ILE C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 440 removed outlier: 3.619A pdb=" N ARG C 440 " --> pdb=" O THR C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 460 removed outlier: 3.558A pdb=" N ARG C 459 " --> pdb=" O GLY C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 4.016A pdb=" N ARG C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 525' Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 576 through 580 Processing helix chain 'C' and resid 587 through 599 removed outlier: 4.076A pdb=" N ARG C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 623 Processing helix chain 'C' and resid 725 through 731 Processing helix chain 'C' and resid 765 through 769 removed outlier: 4.508A pdb=" N ASP C 769 " --> pdb=" O VAL C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 812 Processing helix chain 'C' and resid 906 through 912 removed outlier: 4.211A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 928 removed outlier: 3.508A pdb=" N LEU C 918 " --> pdb=" O PRO C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 947 Processing helix chain 'C' and resid 966 through 976 removed outlier: 3.554A pdb=" N LEU C 970 " --> pdb=" O ARG C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1026 removed outlier: 3.995A pdb=" N LYS C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1044 through 1048 Processing helix chain 'C' and resid 1054 through 1064 removed outlier: 3.683A pdb=" N TYR C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1075 Processing helix chain 'C' and resid 1080 through 1094 removed outlier: 3.838A pdb=" N VAL C1085 " --> pdb=" O VAL C1081 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS C1086 " --> pdb=" O THR C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1104 through 1115 Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 121 through 127 removed outlier: 3.529A pdb=" N LEU D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 147 through 188 Processing helix chain 'D' and resid 192 through 228 Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 256 through 268 removed outlier: 3.905A pdb=" N ALA D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.867A pdb=" N THR D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 removed outlier: 3.695A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 360 removed outlier: 3.513A pdb=" N LEU D 360 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 407 removed outlier: 3.938A pdb=" N LYS D 407 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 417 removed outlier: 3.512A pdb=" N LEU D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 480 through 491 Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 533 removed outlier: 3.629A pdb=" N CYS D 529 " --> pdb=" O HIS D 525 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR D 530 " --> pdb=" O PRO D 526 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE D 532 " --> pdb=" O VAL D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 580 through 589 removed outlier: 3.677A pdb=" N GLY D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 617 Processing helix chain 'D' and resid 636 through 640 removed outlier: 3.555A pdb=" N GLU D 640 " --> pdb=" O ARG D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 672 removed outlier: 3.508A pdb=" N LEU D 672 " --> pdb=" O PHE D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 699 Processing helix chain 'D' and resid 700 through 723 removed outlier: 3.937A pdb=" N GLY D 723 " --> pdb=" O ALA D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 757 removed outlier: 3.611A pdb=" N ARG D 757 " --> pdb=" O LYS D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 788 Processing helix chain 'D' and resid 792 through 800 Processing helix chain 'D' and resid 805 through 814 removed outlier: 3.511A pdb=" N MET D 809 " --> pdb=" O ASN D 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 877 removed outlier: 3.989A pdb=" N GLY D 850 " --> pdb=" O ILE D 846 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS D 853 " --> pdb=" O HIS D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 950 Processing helix chain 'D' and resid 969 through 974 removed outlier: 3.544A pdb=" N TYR D 973 " --> pdb=" O CYS D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 999 removed outlier: 3.676A pdb=" N ILE D 992 " --> pdb=" O ALA D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1005 removed outlier: 4.479A pdb=" N THR D1005 " --> pdb=" O GLY D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1022 through 1031 Processing helix chain 'D' and resid 1100 through 1108 removed outlier: 3.626A pdb=" N VAL D1104 " --> pdb=" O ASN D1100 " (cutoff:3.500A) Processing helix chain 'D' and resid 1109 through 1127 removed outlier: 3.556A pdb=" N SER D1127 " --> pdb=" O LYS D1123 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1145 removed outlier: 4.129A pdb=" N ILE D1137 " --> pdb=" O HIS D1133 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE D1140 " --> pdb=" O HIS D1136 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D1145 " --> pdb=" O ILE D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1180 Processing helix chain 'D' and resid 1192 through 1199 Processing helix chain 'D' and resid 1202 through 1209 Processing helix chain 'D' and resid 1212 through 1223 Processing helix chain 'D' and resid 1231 through 1238 removed outlier: 4.282A pdb=" N ILE D1236 " --> pdb=" O LYS D1232 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE D1237 " --> pdb=" O GLU D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1258 through 1265 Processing helix chain 'E' and resid 15 through 24 removed outlier: 4.174A pdb=" N LEU E 19 " --> pdb=" O PRO E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 45 Processing helix chain 'E' and resid 66 through 78 removed outlier: 3.635A pdb=" N ILE E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 223 Processing helix chain 'F' and resid 229 through 252 Processing helix chain 'F' and resid 257 through 294 removed outlier: 5.091A pdb=" N ARG F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 317 Processing helix chain 'F' and resid 325 through 345 removed outlier: 4.016A pdb=" N TYR F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TRP F 332 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TRP F 333 " --> pdb=" O TYR F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 374 Processing helix chain 'F' and resid 378 through 387 Processing helix chain 'F' and resid 389 through 400 Processing helix chain 'F' and resid 417 through 421 removed outlier: 3.739A pdb=" N LEU F 421 " --> pdb=" O PHE F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 450 Processing helix chain 'F' and resid 451 through 463 Processing helix chain 'F' and resid 471 through 476 removed outlier: 3.511A pdb=" N GLY F 476 " --> pdb=" O LEU F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 498 removed outlier: 3.642A pdb=" N ARG F 487 " --> pdb=" O ARG F 483 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 502 No H-bonds generated for 'chain 'F' and resid 500 through 502' Processing helix chain 'F' and resid 503 through 508 removed outlier: 4.078A pdb=" N ASP F 508 " --> pdb=" O GLN F 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 26 removed outlier: 3.840A pdb=" N ALA G 17 " --> pdb=" O THR G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 43 Processing helix chain 'G' and resid 47 through 62 removed outlier: 4.050A pdb=" N VAL G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 116 Processing helix chain 'G' and resid 130 through 135 Processing helix chain 'H' and resid 13 through 26 Processing helix chain 'H' and resid 32 through 43 Processing helix chain 'H' and resid 47 through 62 Processing helix chain 'H' and resid 101 through 115 removed outlier: 3.840A pdb=" N GLU H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 135 removed outlier: 4.228A pdb=" N ALA H 134 " --> pdb=" O CYS H 130 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY H 135 " --> pdb=" O ALA H 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 130 through 135' Processing helix chain 'M' and resid 13 through 26 removed outlier: 3.509A pdb=" N VAL M 26 " --> pdb=" O ALA M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 43 Processing helix chain 'M' and resid 47 through 62 Processing helix chain 'M' and resid 101 through 116 removed outlier: 3.892A pdb=" N GLU M 105 " --> pdb=" O GLY M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 135 Processing helix chain 'N' and resid 13 through 26 Processing helix chain 'N' and resid 32 through 43 Processing helix chain 'N' and resid 47 through 62 Processing helix chain 'N' and resid 101 through 116 removed outlier: 4.201A pdb=" N GLU N 105 " --> pdb=" O GLY N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 135 removed outlier: 4.123A pdb=" N ALA N 134 " --> pdb=" O CYS N 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 5.622A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 3.634A pdb=" N SER A 53 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 4.370A pdb=" N ASP B 188 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N THR B 181 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ASP B 190 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU B 179 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU B 192 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS B 177 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL B 194 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR B 175 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL B 196 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS B 173 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 198 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 171 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 99 removed outlier: 3.742A pdb=" N SER B 53 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLU B 141 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL B 51 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLY B 143 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA B 49 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA8, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.668A pdb=" N GLY B 103 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.787A pdb=" N VAL B 147 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 166 " --> pdb=" O VAL B 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.363A pdb=" N ILE C 23 " --> pdb=" O ALA C 958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 100 removed outlier: 5.242A pdb=" N LEU C 93 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR C 128 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N PHE C 95 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLU C 126 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASP C 97 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA C 119 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASP C 144 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU C 121 " --> pdb=" O MET C 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 169 Processing sheet with id=AB5, first strand: chain 'C' and resid 172 through 180 removed outlier: 3.601A pdb=" N ASP C 180 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS C 185 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE C 188 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU C 200 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AB7, first strand: chain 'C' and resid 441 through 442 Processing sheet with id=AB8, first strand: chain 'C' and resid 491 through 492 removed outlier: 6.922A pdb=" N ILE C 498 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU C 517 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR C 500 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP C 515 " --> pdb=" O THR C 500 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR C 502 " --> pdb=" O ASP C 513 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP C 513 " --> pdb=" O TYR C 502 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS C 504 " --> pdb=" O THR C 511 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 491 through 492 Processing sheet with id=AC1, first strand: chain 'C' and resid 628 through 629 removed outlier: 6.997A pdb=" N VAL C 628 " --> pdb=" O LEU C 688 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 634 through 639 removed outlier: 7.093A pdb=" N THR C 645 " --> pdb=" O GLN C 637 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N VAL C 639 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N TYR C 643 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 694 through 695 Processing sheet with id=AC4, first strand: chain 'C' and resid 870 through 872 removed outlier: 7.148A pdb=" N ILE C 721 " --> pdb=" O SER C 882 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE C 884 " --> pdb=" O ILE C 721 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU C 723 " --> pdb=" O ILE C 884 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE C 722 " --> pdb=" O ILE C 902 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N ILE C 901 " --> pdb=" O ASN C 704 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU C 706 " --> pdb=" O ILE C 901 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU C 903 " --> pdb=" O LEU C 706 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA C 708 " --> pdb=" O LEU C 903 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER C1009 " --> pdb=" O PHE C 709 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 734 through 744 removed outlier: 4.288A pdb=" N GLY C 835 " --> pdb=" O TYR C 858 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA C 860 " --> pdb=" O VAL C 833 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N VAL C 833 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N LYS C 862 " --> pdb=" O GLY C 831 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N GLY C 831 " --> pdb=" O LYS C 862 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY C 831 " --> pdb=" O VAL C 782 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 754 through 755 Processing sheet with id=AC7, first strand: chain 'C' and resid 787 through 789 removed outlier: 3.541A pdb=" N LEU C 788 " --> pdb=" O LEU C 823 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU C 823 " --> pdb=" O LEU C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 892 through 893 Processing sheet with id=AC9, first strand: chain 'C' and resid 1027 through 1029 removed outlier: 3.714A pdb=" N ALA D 426 " --> pdb=" O VAL D 543 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER D 428 " --> pdb=" O MET D 541 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1052 through 1053 Processing sheet with id=AD2, first strand: chain 'C' and resid 1123 through 1124 Processing sheet with id=AD3, first strand: chain 'D' and resid 9 through 10 removed outlier: 3.797A pdb=" N ASP D1226 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 94 through 96 Processing sheet with id=AD5, first strand: chain 'D' and resid 234 through 235 removed outlier: 5.300A pdb=" N ILE D 136 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 336 through 337 removed outlier: 3.679A pdb=" N THR D 337 " --> pdb=" O ILE F 404 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 430 through 432 Processing sheet with id=AD8, first strand: chain 'D' and resid 443 through 444 removed outlier: 5.643A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 566 through 567 removed outlier: 3.872A pdb=" N ARG D 572 " --> pdb=" O LYS D 567 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 603 through 604 Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 821 removed outlier: 3.676A pdb=" N GLU D 825 " --> pdb=" O ASN D 821 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 892 through 895 removed outlier: 4.099A pdb=" N MET D 919 " --> pdb=" O ARG D 957 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1070 through 1073 removed outlier: 3.635A pdb=" N GLY D1046 " --> pdb=" O VAL D1088 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1163 through 1165 Processing sheet with id=AE6, first strand: chain 'D' and resid 1253 through 1257 removed outlier: 3.595A pdb=" N ARG D1254 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU E 83 " --> pdb=" O ARG D1254 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 30 through 31 Processing sheet with id=AE8, first strand: chain 'G' and resid 96 through 99 removed outlier: 5.174A pdb=" N HIS G 87 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE G 126 " --> pdb=" O HIS G 87 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N HIS H 87 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N GLY H 128 " --> pdb=" O HIS H 87 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL H 89 " --> pdb=" O GLY H 128 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 30 through 31 Processing sheet with id=AF1, first strand: chain 'M' and resid 65 through 68 Processing sheet with id=AF2, first strand: chain 'M' and resid 96 through 99 removed outlier: 5.146A pdb=" N HIS M 87 " --> pdb=" O VAL M 124 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE M 126 " --> pdb=" O HIS M 87 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE N 127 " --> pdb=" O ALA M 121 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR M 123 " --> pdb=" O GLU N 125 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU N 125 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N HIS N 87 " --> pdb=" O ILE N 126 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 30 through 31 1332 hydrogen bonds defined for protein. 3786 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 180 hydrogen bonds 356 hydrogen bond angles 0 basepair planarities 68 basepair parallelities 116 stacking parallelities Total time for adding SS restraints: 16.53 Time building geometry restraints manager: 16.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10044 1.34 - 1.46: 5930 1.46 - 1.58: 16933 1.58 - 1.70: 342 1.70 - 1.82: 189 Bond restraints: 33438 Sorted by residual: bond pdb=" O3' DC O 29 " pdb=" P DG O 30 " ideal model delta sigma weight residual 1.607 1.653 -0.046 1.50e-02 4.44e+03 9.32e+00 bond pdb=" C ALA A 111 " pdb=" N PRO A 112 " ideal model delta sigma weight residual 1.329 1.362 -0.033 1.18e-02 7.18e+03 7.76e+00 bond pdb=" O3' DA P 63 " pdb=" P DA P 64 " ideal model delta sigma weight residual 1.607 1.645 -0.038 1.50e-02 4.44e+03 6.28e+00 bond pdb=" CA ILE B 46 " pdb=" C ILE B 46 " ideal model delta sigma weight residual 1.524 1.554 -0.029 1.20e-02 6.94e+03 5.99e+00 bond pdb=" O3' DT O 22 " pdb=" P DC O 23 " ideal model delta sigma weight residual 1.607 1.642 -0.035 1.50e-02 4.44e+03 5.53e+00 ... (remaining 33433 not shown) Histogram of bond angle deviations from ideal: 97.13 - 104.79: 1074 104.79 - 112.45: 17370 112.45 - 120.10: 13488 120.10 - 127.76: 13541 127.76 - 135.42: 506 Bond angle restraints: 45979 Sorted by residual: angle pdb=" N GLN A 157 " pdb=" CA GLN A 157 " pdb=" C GLN A 157 " ideal model delta sigma weight residual 111.28 118.88 -7.60 1.09e+00 8.42e-01 4.87e+01 angle pdb=" N TYR A 168 " pdb=" CA TYR A 168 " pdb=" C TYR A 168 " ideal model delta sigma weight residual 111.28 118.34 -7.06 1.09e+00 8.42e-01 4.19e+01 angle pdb=" N VAL A 155 " pdb=" CA VAL A 155 " pdb=" C VAL A 155 " ideal model delta sigma weight residual 106.61 117.72 -11.11 1.78e+00 3.16e-01 3.90e+01 angle pdb=" N ASP D 878 " pdb=" CA ASP D 878 " pdb=" C ASP D 878 " ideal model delta sigma weight residual 111.28 117.67 -6.39 1.09e+00 8.42e-01 3.44e+01 angle pdb=" N VAL C 510 " pdb=" CA VAL C 510 " pdb=" C VAL C 510 " ideal model delta sigma weight residual 106.85 114.99 -8.14 1.42e+00 4.96e-01 3.29e+01 ... (remaining 45974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 18694 35.94 - 71.87: 1163 71.87 - 107.81: 53 107.81 - 143.74: 4 143.74 - 179.68: 13 Dihedral angle restraints: 19927 sinusoidal: 9244 harmonic: 10683 Sorted by residual: dihedral pdb=" C ASP E 24 " pdb=" N ASP E 24 " pdb=" CA ASP E 24 " pdb=" CB ASP E 24 " ideal model delta harmonic sigma weight residual -122.60 -137.22 14.62 0 2.50e+00 1.60e-01 3.42e+01 dihedral pdb=" N ASP E 24 " pdb=" C ASP E 24 " pdb=" CA ASP E 24 " pdb=" CB ASP E 24 " ideal model delta harmonic sigma weight residual 122.80 136.86 -14.06 0 2.50e+00 1.60e-01 3.17e+01 dihedral pdb=" CA ASP D 537 " pdb=" C ASP D 537 " pdb=" N GLY D 538 " pdb=" CA GLY D 538 " ideal model delta harmonic sigma weight residual 180.00 158.02 21.98 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 19924 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 4938 0.102 - 0.204: 261 0.204 - 0.306: 22 0.306 - 0.408: 3 0.408 - 0.510: 1 Chirality restraints: 5225 Sorted by residual: chirality pdb=" CA ASP E 24 " pdb=" N ASP E 24 " pdb=" C ASP E 24 " pdb=" CB ASP E 24 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" CA LYS A 153 " pdb=" N LYS A 153 " pdb=" C LYS A 153 " pdb=" CB LYS A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA GLU C 473 " pdb=" N GLU C 473 " pdb=" C GLU C 473 " pdb=" CB GLU C 473 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 ... (remaining 5222 not shown) Planarity restraints: 5422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 407 " 0.079 5.00e-02 4.00e+02 1.18e-01 2.21e+01 pdb=" N PRO C 408 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO C 408 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO C 408 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG O 72 " 0.038 2.00e-02 2.50e+03 1.66e-02 8.27e+00 pdb=" N9 DG O 72 " -0.039 2.00e-02 2.50e+03 pdb=" C8 DG O 72 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG O 72 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG O 72 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG O 72 " 0.012 2.00e-02 2.50e+03 pdb=" O6 DG O 72 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG O 72 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG O 72 " -0.003 2.00e-02 2.50e+03 pdb=" N2 DG O 72 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DG O 72 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DG O 72 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG P 49 " 0.009 2.00e-02 2.50e+03 1.51e-02 6.80e+00 pdb=" N9 DG P 49 " -0.003 2.00e-02 2.50e+03 pdb=" C8 DG P 49 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG P 49 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DG P 49 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG P 49 " 0.000 2.00e-02 2.50e+03 pdb=" O6 DG P 49 " -0.000 2.00e-02 2.50e+03 pdb=" N1 DG P 49 " 0.015 2.00e-02 2.50e+03 pdb=" C2 DG P 49 " -0.043 2.00e-02 2.50e+03 pdb=" N2 DG P 49 " 0.022 2.00e-02 2.50e+03 pdb=" N3 DG P 49 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG P 49 " 0.003 2.00e-02 2.50e+03 ... (remaining 5419 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 202 2.51 - 3.11: 24973 3.11 - 3.70: 53572 3.70 - 4.30: 70421 4.30 - 4.90: 113458 Nonbonded interactions: 262626 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D1401 " model vdw 1.912 2.170 nonbonded pdb=" O3' G Q 5 " pdb="MG MG D1401 " model vdw 1.915 2.170 nonbonded pdb=" OE2 GLU N 105 " pdb="ZN ZN N 203 " model vdw 1.975 2.230 nonbonded pdb=" OD2 ASP N 65 " pdb="ZN ZN N 202 " model vdw 1.981 2.230 nonbonded pdb=" OD2 ASP D 535 " pdb="MG MG D1401 " model vdw 2.048 2.170 ... (remaining 262621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 2 through 227) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.100 Check model and map are aligned: 0.540 Set scattering table: 0.310 Process input model: 104.850 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 33438 Z= 0.293 Angle : 0.797 11.110 45979 Z= 0.461 Chirality : 0.051 0.510 5225 Planarity : 0.005 0.118 5422 Dihedral : 20.730 179.680 13051 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.87 % Allowed : 22.12 % Favored : 77.01 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3713 helix: 1.24 (0.14), residues: 1452 sheet: -0.88 (0.23), residues: 465 loop : -0.89 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 924 HIS 0.009 0.001 HIS H 85 PHE 0.018 0.002 PHE A 17 TYR 0.023 0.002 TYR E 32 ARG 0.009 0.000 ARG C 808 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 434 time to evaluate : 3.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.7205 (mmtt) cc_final: 0.6939 (mmtt) REVERT: C 142 MET cc_start: 0.6608 (mmm) cc_final: 0.6094 (mmm) REVERT: C 550 ARG cc_start: 0.6347 (ttm110) cc_final: 0.5875 (mtp85) REVERT: C 821 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8050 (t) REVERT: D 59 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6659 (mt-10) REVERT: D 296 LEU cc_start: 0.7434 (mt) cc_final: 0.7096 (mt) REVERT: D 861 ARG cc_start: 0.6222 (OUTLIER) cc_final: 0.6001 (mmt-90) REVERT: D 888 THR cc_start: 0.7640 (t) cc_final: 0.7413 (t) REVERT: D 916 TYR cc_start: 0.7374 (m-10) cc_final: 0.6848 (m-80) REVERT: E 74 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7760 (mt-10) REVERT: F 245 PHE cc_start: 0.8157 (m-10) cc_final: 0.7941 (m-80) REVERT: F 282 ASN cc_start: 0.6488 (m110) cc_final: 0.6105 (t0) outliers start: 27 outliers final: 8 residues processed: 449 average time/residue: 0.5059 time to fit residues: 348.8256 Evaluate side-chains 337 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 327 time to evaluate : 3.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain F residue 460 MET Chi-restraints excluded: chain F residue 485 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 30.0000 chunk 291 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 196 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 301 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 224 optimal weight: 0.9990 chunk 349 optimal weight: 30.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 HIS C 424 GLN C 465 HIS ** C 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 980 ASN C1040 GLN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN D1122 GLN ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 ASN F 305 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 33438 Z= 0.403 Angle : 0.737 8.546 45979 Z= 0.393 Chirality : 0.047 0.207 5225 Planarity : 0.006 0.083 5422 Dihedral : 20.976 178.828 5965 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.51 % Allowed : 21.70 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.13), residues: 3713 helix: 0.99 (0.13), residues: 1500 sheet: -0.92 (0.23), residues: 472 loop : -1.03 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 712 HIS 0.023 0.001 HIS F 354 PHE 0.020 0.002 PHE D 512 TYR 0.025 0.002 TYR D 106 ARG 0.012 0.001 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 361 time to evaluate : 3.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 MET cc_start: 0.6621 (ttm) cc_final: 0.6370 (ttp) REVERT: C 27 LYS cc_start: 0.7529 (mmtt) cc_final: 0.7185 (mmtt) REVERT: C 191 LYS cc_start: 0.7566 (pttt) cc_final: 0.7070 (pttt) REVERT: C 243 TYR cc_start: 0.8301 (m-80) cc_final: 0.7723 (m-80) REVERT: C 366 ASN cc_start: 0.6647 (OUTLIER) cc_final: 0.6399 (p0) REVERT: C 382 MET cc_start: 0.8106 (tmm) cc_final: 0.7458 (tmm) REVERT: C 565 MET cc_start: 0.7600 (ppp) cc_final: 0.7155 (ppp) REVERT: C 930 TRP cc_start: 0.7927 (p90) cc_final: 0.7639 (p90) REVERT: C 1061 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7880 (tp) REVERT: C 1112 GLU cc_start: 0.6838 (tt0) cc_final: 0.6439 (tt0) REVERT: D 59 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6902 (mt-10) REVERT: D 474 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7740 (ttp80) REVERT: D 861 ARG cc_start: 0.6152 (OUTLIER) cc_final: 0.5851 (mmp-170) REVERT: D 916 TYR cc_start: 0.7788 (m-10) cc_final: 0.7352 (m-80) REVERT: F 245 PHE cc_start: 0.8306 (m-10) cc_final: 0.7992 (m-80) REVERT: F 282 ASN cc_start: 0.7201 (m-40) cc_final: 0.6696 (t0) REVERT: H 25 GLU cc_start: 0.0283 (OUTLIER) cc_final: 0.0037 (pt0) REVERT: N 38 MET cc_start: -0.1135 (ptt) cc_final: -0.2050 (mmp) REVERT: N 79 CYS cc_start: 0.2875 (OUTLIER) cc_final: 0.1365 (p) outliers start: 140 outliers final: 82 residues processed: 470 average time/residue: 0.4575 time to fit residues: 344.6269 Evaluate side-chains 397 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 310 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 366 ASN Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 593 MET Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 840 ASP Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 963 ASP Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1024 ASP Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 788 PHE Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 879 VAL Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 1065 ASP Chi-restraints excluded: chain D residue 1100 ASN Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1132 ILE Chi-restraints excluded: chain D residue 1168 LYS Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 405 SER Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 490 GLU Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 194 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 290 optimal weight: 4.9990 chunk 238 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 350 optimal weight: 50.0000 chunk 378 optimal weight: 2.9990 chunk 311 optimal weight: 3.9990 chunk 347 optimal weight: 10.0000 chunk 119 optimal weight: 0.0470 chunk 280 optimal weight: 5.9990 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN A 152 ASN B 185 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 HIS ** C 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN D 965 GLN ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 488 GLN H 86 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33438 Z= 0.265 Angle : 0.637 9.005 45979 Z= 0.339 Chirality : 0.043 0.186 5225 Planarity : 0.005 0.064 5422 Dihedral : 20.836 179.969 5960 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.54 % Allowed : 23.31 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.13), residues: 3713 helix: 1.14 (0.13), residues: 1500 sheet: -0.69 (0.24), residues: 446 loop : -1.01 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 712 HIS 0.013 0.001 HIS F 354 PHE 0.015 0.002 PHE F 462 TYR 0.041 0.002 TYR E 32 ARG 0.014 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 340 time to evaluate : 3.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.8520 (tp) cc_final: 0.8303 (tp) REVERT: B 202 MET cc_start: 0.6951 (ttm) cc_final: 0.6726 (ttp) REVERT: C 27 LYS cc_start: 0.7423 (mmtt) cc_final: 0.7132 (mmtt) REVERT: C 196 ARG cc_start: 0.7104 (ptp-170) cc_final: 0.6757 (ptp-170) REVERT: C 243 TYR cc_start: 0.8218 (m-80) cc_final: 0.7599 (m-80) REVERT: C 292 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8543 (mtmm) REVERT: C 382 MET cc_start: 0.8323 (tmm) cc_final: 0.7607 (tmm) REVERT: C 565 MET cc_start: 0.7620 (ppp) cc_final: 0.7067 (ptm) REVERT: C 598 MET cc_start: 0.7747 (mtp) cc_final: 0.7466 (mtp) REVERT: C 718 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7692 (mm-30) REVERT: C 930 TRP cc_start: 0.7770 (p90) cc_final: 0.7490 (p90) REVERT: D 30 LYS cc_start: 0.8556 (mtmt) cc_final: 0.8329 (mtpt) REVERT: D 59 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6713 (mt-10) REVERT: D 861 ARG cc_start: 0.5800 (OUTLIER) cc_final: 0.5178 (mmp-170) REVERT: D 916 TYR cc_start: 0.7651 (m-10) cc_final: 0.7255 (m-80) REVERT: D 1005 THR cc_start: 0.3137 (OUTLIER) cc_final: 0.2846 (m) REVERT: F 245 PHE cc_start: 0.8266 (m-10) cc_final: 0.7771 (m-80) REVERT: F 282 ASN cc_start: 0.6995 (m-40) cc_final: 0.6618 (t0) REVERT: H 25 GLU cc_start: 0.0336 (OUTLIER) cc_final: 0.0041 (pt0) REVERT: N 79 CYS cc_start: 0.3087 (OUTLIER) cc_final: 0.1618 (p) outliers start: 141 outliers final: 92 residues processed: 453 average time/residue: 0.4986 time to fit residues: 365.2948 Evaluate side-chains 409 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 312 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 718 GLU Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 840 ASP Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 1024 ASP Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain D residue 396 ASN Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 846 ILE Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 971 MET Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 1005 THR Chi-restraints excluded: chain D residue 1065 ASP Chi-restraints excluded: chain D residue 1100 ASN Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1147 ARG Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 405 SER Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 346 optimal weight: 8.9990 chunk 263 optimal weight: 8.9990 chunk 181 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 351 optimal weight: 30.0000 chunk 372 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 333 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 119 HIS A 152 ASN ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 396 ASN D 416 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 544 HIS ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.105 33438 Z= 0.561 Angle : 0.826 13.135 45979 Z= 0.434 Chirality : 0.049 0.231 5225 Planarity : 0.007 0.091 5422 Dihedral : 20.861 179.906 5960 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 7.24 % Allowed : 23.44 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 3713 helix: 0.58 (0.13), residues: 1490 sheet: -1.07 (0.23), residues: 462 loop : -1.36 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 712 HIS 0.010 0.002 HIS A 61 PHE 0.025 0.003 PHE C 359 TYR 0.025 0.003 TYR C 174 ARG 0.014 0.001 ARG C 816 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 328 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASP cc_start: 0.7100 (m-30) cc_final: 0.6874 (m-30) REVERT: A 134 LEU cc_start: 0.8551 (tp) cc_final: 0.8323 (tp) REVERT: B 120 ASN cc_start: 0.7921 (p0) cc_final: 0.7617 (p0) REVERT: B 202 MET cc_start: 0.7237 (ttm) cc_final: 0.6979 (ttp) REVERT: C 27 LYS cc_start: 0.7599 (mmtt) cc_final: 0.7246 (mmtt) REVERT: C 49 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8363 (mp) REVERT: C 243 TYR cc_start: 0.8381 (m-80) cc_final: 0.7665 (m-80) REVERT: C 292 LYS cc_start: 0.9107 (mmmt) cc_final: 0.8902 (mmmt) REVERT: C 366 ASN cc_start: 0.7069 (OUTLIER) cc_final: 0.6860 (p0) REVERT: C 382 MET cc_start: 0.8542 (tmm) cc_final: 0.7715 (tmm) REVERT: C 413 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.7007 (tt) REVERT: C 565 MET cc_start: 0.8053 (ppp) cc_final: 0.7719 (ppp) REVERT: C 718 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7905 (mm-30) REVERT: C 969 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.5644 (mp0) REVERT: C 1048 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8317 (m-80) REVERT: D 9 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6882 (pt0) REVERT: D 30 LYS cc_start: 0.8670 (mtmt) cc_final: 0.8368 (mtpt) REVERT: D 59 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7156 (mt-10) REVERT: D 141 GLU cc_start: 0.8258 (tp30) cc_final: 0.8055 (tp30) REVERT: D 296 LEU cc_start: 0.7388 (mt) cc_final: 0.7127 (mt) REVERT: D 474 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7586 (tmt170) REVERT: D 533 ASN cc_start: 0.7505 (t0) cc_final: 0.7232 (m110) REVERT: D 861 ARG cc_start: 0.5685 (OUTLIER) cc_final: 0.5163 (mmp-170) REVERT: D 910 ASP cc_start: 0.7312 (p0) cc_final: 0.7003 (p0) REVERT: D 916 TYR cc_start: 0.8087 (m-10) cc_final: 0.7802 (m-80) REVERT: D 997 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8821 (mt) REVERT: D 1120 GLU cc_start: 0.6667 (tp30) cc_final: 0.6361 (tp30) REVERT: D 1169 PHE cc_start: 0.8667 (t80) cc_final: 0.8376 (t80) REVERT: E 32 TYR cc_start: 0.6289 (OUTLIER) cc_final: 0.6046 (t80) REVERT: E 83 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7541 (tm-30) REVERT: F 245 PHE cc_start: 0.8452 (m-10) cc_final: 0.8128 (m-80) REVERT: F 490 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8242 (tp30) REVERT: H 25 GLU cc_start: 0.0317 (OUTLIER) cc_final: 0.0017 (pt0) REVERT: N 79 CYS cc_start: 0.2794 (OUTLIER) cc_final: 0.1542 (p) outliers start: 225 outliers final: 145 residues processed: 513 average time/residue: 0.4678 time to fit residues: 379.6034 Evaluate side-chains 455 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 298 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 366 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 718 GLU Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 840 ASP Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 963 ASP Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1024 ASP Chi-restraints excluded: chain C residue 1031 THR Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 396 ASN Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 788 PHE Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 841 VAL Chi-restraints excluded: chain D residue 846 ILE Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 875 VAL Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 971 MET Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1055 LYS Chi-restraints excluded: chain D residue 1065 ASP Chi-restraints excluded: chain D residue 1072 PHE Chi-restraints excluded: chain D residue 1100 ASN Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1132 ILE Chi-restraints excluded: chain D residue 1182 HIS Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1253 ILE Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 405 SER Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 309 optimal weight: 0.7980 chunk 211 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 277 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 317 optimal weight: 0.1980 chunk 257 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 190 optimal weight: 0.6980 chunk 334 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS A 152 ASN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 GLN C 428 GLN ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 GLN D 341 ASN D 965 GLN ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33438 Z= 0.200 Angle : 0.651 12.272 45979 Z= 0.340 Chirality : 0.042 0.289 5225 Planarity : 0.004 0.062 5422 Dihedral : 20.712 179.765 5958 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.05 % Allowed : 25.47 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3713 helix: 1.06 (0.13), residues: 1500 sheet: -0.83 (0.23), residues: 463 loop : -1.16 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 773 HIS 0.008 0.001 HIS F 354 PHE 0.017 0.001 PHE B 17 TYR 0.029 0.001 TYR E 32 ARG 0.006 0.000 ARG C 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 329 time to evaluate : 3.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.4967 (OUTLIER) cc_final: 0.4715 (pm20) REVERT: A 109 ASP cc_start: 0.7111 (m-30) cc_final: 0.6839 (m-30) REVERT: A 134 LEU cc_start: 0.8369 (tp) cc_final: 0.8105 (tp) REVERT: C 27 LYS cc_start: 0.7459 (mmtt) cc_final: 0.7214 (mmtt) REVERT: C 142 MET cc_start: 0.6470 (mmm) cc_final: 0.6213 (mmm) REVERT: C 243 TYR cc_start: 0.8137 (m-80) cc_final: 0.7203 (m-10) REVERT: C 292 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8762 (mmmt) REVERT: C 382 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.7723 (tmm) REVERT: C 565 MET cc_start: 0.8005 (ppp) cc_final: 0.7394 (ptm) REVERT: C 1048 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8346 (m-80) REVERT: D 9 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6441 (pt0) REVERT: D 30 LYS cc_start: 0.8639 (mtmt) cc_final: 0.8037 (mtpp) REVERT: D 59 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7142 (tt0) REVERT: D 141 GLU cc_start: 0.8369 (tp30) cc_final: 0.7944 (tp30) REVERT: D 220 ASP cc_start: 0.8350 (m-30) cc_final: 0.8140 (m-30) REVERT: D 296 LEU cc_start: 0.7263 (mt) cc_final: 0.6998 (mt) REVERT: D 320 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8509 (mt) REVERT: D 474 ARG cc_start: 0.7848 (ttp80) cc_final: 0.7515 (ttp80) REVERT: D 861 ARG cc_start: 0.5607 (OUTLIER) cc_final: 0.5174 (mmp-170) REVERT: D 916 TYR cc_start: 0.7785 (m-10) cc_final: 0.7526 (m-10) REVERT: D 997 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8486 (mt) REVERT: D 1076 LYS cc_start: 0.8835 (mmmt) cc_final: 0.8561 (mmmt) REVERT: F 245 PHE cc_start: 0.8351 (m-10) cc_final: 0.8036 (m-80) REVERT: F 282 ASN cc_start: 0.7109 (m-40) cc_final: 0.6828 (t0) REVERT: F 490 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8265 (tp30) REVERT: H 25 GLU cc_start: 0.0366 (OUTLIER) cc_final: 0.0109 (pt0) REVERT: N 38 MET cc_start: 0.0217 (pmm) cc_final: -0.1275 (mmm) REVERT: N 79 CYS cc_start: 0.2815 (OUTLIER) cc_final: 0.1578 (p) outliers start: 157 outliers final: 90 residues processed: 460 average time/residue: 0.4793 time to fit residues: 350.8969 Evaluate side-chains 406 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 307 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 647 THR Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 840 ASP Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1024 ASP Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1104 GLU Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 762 LYS Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 841 VAL Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 971 MET Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain D residue 1095 THR Chi-restraints excluded: chain D residue 1100 ASN Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1147 ARG Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain N residue 36 HIS Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 125 optimal weight: 7.9990 chunk 335 optimal weight: 0.0870 chunk 73 optimal weight: 0.7980 chunk 218 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 372 optimal weight: 20.0000 chunk 309 optimal weight: 0.4980 chunk 172 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 ASN ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 GLN C 596 ASN ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1116 HIS ** F 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33438 Z= 0.245 Angle : 0.647 14.017 45979 Z= 0.338 Chirality : 0.043 0.283 5225 Planarity : 0.004 0.057 5422 Dihedral : 20.630 179.576 5956 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.47 % Allowed : 25.50 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3713 helix: 1.12 (0.13), residues: 1504 sheet: -0.77 (0.24), residues: 460 loop : -1.13 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 718 HIS 0.005 0.001 HIS C 741 PHE 0.029 0.002 PHE D 268 TYR 0.027 0.001 TYR E 32 ARG 0.013 0.000 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 322 time to evaluate : 3.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7372 (p0) cc_final: 0.7061 (p0) REVERT: B 208 MET cc_start: 0.8150 (mtm) cc_final: 0.7947 (mtt) REVERT: C 27 LYS cc_start: 0.7456 (mmtt) cc_final: 0.7176 (mmtt) REVERT: C 243 TYR cc_start: 0.8130 (m-80) cc_final: 0.7528 (m-80) REVERT: C 382 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7739 (tmm) REVERT: C 413 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6873 (tt) REVERT: C 565 MET cc_start: 0.8107 (ppp) cc_final: 0.7601 (ptm) REVERT: C 718 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7745 (mm-30) REVERT: C 1036 MET cc_start: 0.7602 (mpp) cc_final: 0.7395 (mpt) REVERT: C 1048 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: C 1061 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7484 (tp) REVERT: D 9 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6477 (pt0) REVERT: D 30 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8576 (mtmt) REVERT: D 59 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6835 (mt-10) REVERT: D 86 LYS cc_start: 0.8095 (ttpp) cc_final: 0.7826 (tttp) REVERT: D 141 GLU cc_start: 0.8448 (tp30) cc_final: 0.7975 (tp30) REVERT: D 214 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.8885 (mtt-85) REVERT: D 220 ASP cc_start: 0.8364 (m-30) cc_final: 0.8131 (m-30) REVERT: D 296 LEU cc_start: 0.7323 (mt) cc_final: 0.7030 (mt) REVERT: D 320 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8541 (mt) REVERT: D 506 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8575 (ptt180) REVERT: D 861 ARG cc_start: 0.5443 (OUTLIER) cc_final: 0.4944 (mmp-170) REVERT: D 902 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7656 (p0) REVERT: D 916 TYR cc_start: 0.7888 (m-10) cc_final: 0.7604 (m-80) REVERT: D 997 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8558 (mt) REVERT: F 282 ASN cc_start: 0.7057 (m-40) cc_final: 0.6774 (t0) REVERT: F 490 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8262 (tp30) REVERT: H 25 GLU cc_start: 0.0366 (OUTLIER) cc_final: 0.0127 (pt0) REVERT: N 79 CYS cc_start: 0.3014 (OUTLIER) cc_final: 0.1747 (p) outliers start: 170 outliers final: 117 residues processed: 460 average time/residue: 0.4541 time to fit residues: 331.5207 Evaluate side-chains 431 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 300 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 718 GLU Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 840 ASP Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 963 ASP Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1024 ASP Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1104 GLU Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 762 LYS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 841 VAL Chi-restraints excluded: chain D residue 846 ILE Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 902 ASP Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 971 MET Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1055 LYS Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain D residue 1095 THR Chi-restraints excluded: chain D residue 1100 ASN Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1147 ARG Chi-restraints excluded: chain D residue 1182 HIS Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain N residue 36 HIS Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 359 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 272 optimal weight: 5.9990 chunk 210 optimal weight: 0.9990 chunk 313 optimal weight: 0.0470 chunk 208 optimal weight: 0.7980 chunk 371 optimal weight: 20.0000 chunk 232 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33438 Z= 0.253 Angle : 0.659 14.134 45979 Z= 0.344 Chirality : 0.043 0.305 5225 Planarity : 0.005 0.080 5422 Dihedral : 20.575 179.668 5956 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.54 % Allowed : 25.92 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3713 helix: 1.12 (0.13), residues: 1504 sheet: -0.76 (0.24), residues: 462 loop : -1.13 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 924 HIS 0.005 0.001 HIS D1116 PHE 0.056 0.002 PHE F 245 TYR 0.031 0.002 TYR C1034 ARG 0.010 0.000 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 310 time to evaluate : 3.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7406 (p0) cc_final: 0.7068 (p0) REVERT: B 208 MET cc_start: 0.8376 (mtm) cc_final: 0.8108 (mtt) REVERT: C 27 LYS cc_start: 0.7409 (mmtt) cc_final: 0.7150 (mmtt) REVERT: C 243 TYR cc_start: 0.8134 (m-80) cc_final: 0.7574 (m-80) REVERT: C 292 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8612 (mtmm) REVERT: C 382 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7897 (tmm) REVERT: C 413 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6843 (tt) REVERT: C 426 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7997 (tpt) REVERT: C 565 MET cc_start: 0.8089 (ppp) cc_final: 0.7559 (ptm) REVERT: C 616 MET cc_start: 0.6726 (ttt) cc_final: 0.6200 (ttt) REVERT: C 718 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7725 (mm-30) REVERT: C 1036 MET cc_start: 0.7594 (mpp) cc_final: 0.7368 (mpt) REVERT: C 1048 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: C 1061 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7490 (tp) REVERT: D 9 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6477 (pt0) REVERT: D 30 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8429 (mtpt) REVERT: D 141 GLU cc_start: 0.8474 (tp30) cc_final: 0.7994 (tp30) REVERT: D 296 LEU cc_start: 0.7354 (mt) cc_final: 0.6780 (mt) REVERT: D 320 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8532 (mt) REVERT: D 506 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8559 (ptt180) REVERT: D 815 MET cc_start: 0.8639 (ptm) cc_final: 0.8286 (ptm) REVERT: D 861 ARG cc_start: 0.5430 (OUTLIER) cc_final: 0.4784 (mmt-90) REVERT: D 902 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7651 (p0) REVERT: D 916 TYR cc_start: 0.7881 (m-10) cc_final: 0.7649 (m-80) REVERT: D 997 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8424 (mt) REVERT: D 1076 LYS cc_start: 0.8694 (mmmt) cc_final: 0.8428 (mmmt) REVERT: E 18 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: F 245 PHE cc_start: 0.8475 (m-80) cc_final: 0.8259 (m-80) REVERT: F 282 ASN cc_start: 0.7231 (m-40) cc_final: 0.6920 (t0) REVERT: F 490 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8281 (tp30) REVERT: H 25 GLU cc_start: 0.0395 (OUTLIER) cc_final: 0.0171 (pt0) REVERT: N 79 CYS cc_start: 0.3007 (OUTLIER) cc_final: 0.1792 (p) outliers start: 172 outliers final: 128 residues processed: 452 average time/residue: 0.4617 time to fit residues: 333.2847 Evaluate side-chains 442 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 299 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 718 GLU Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 840 ASP Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 963 ASP Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1024 ASP Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1104 GLU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 567 LYS Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 762 LYS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 841 VAL Chi-restraints excluded: chain D residue 846 ILE Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 902 ASP Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 971 MET Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1055 LYS Chi-restraints excluded: chain D residue 1095 THR Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1132 ILE Chi-restraints excluded: chain D residue 1147 ARG Chi-restraints excluded: chain D residue 1182 HIS Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1217 THR Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain N residue 36 HIS Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 229 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 221 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 72 optimal weight: 0.2980 chunk 71 optimal weight: 0.9980 chunk 235 optimal weight: 0.8980 chunk 252 optimal weight: 0.6980 chunk 183 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 291 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33438 Z= 0.203 Angle : 0.635 14.836 45979 Z= 0.331 Chirality : 0.042 0.317 5225 Planarity : 0.004 0.071 5422 Dihedral : 20.487 179.528 5954 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.38 % Allowed : 27.08 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3713 helix: 1.24 (0.13), residues: 1497 sheet: -0.67 (0.24), residues: 466 loop : -1.07 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 924 HIS 0.005 0.001 HIS D1116 PHE 0.038 0.001 PHE F 245 TYR 0.028 0.001 TYR E 32 ARG 0.006 0.000 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 321 time to evaluate : 3.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7364 (p0) cc_final: 0.7021 (p0) REVERT: C 27 LYS cc_start: 0.7351 (mmtt) cc_final: 0.7111 (mmtt) REVERT: C 113 ARG cc_start: 0.7742 (mtm-85) cc_final: 0.7485 (mtt90) REVERT: C 243 TYR cc_start: 0.7964 (m-80) cc_final: 0.7425 (m-80) REVERT: C 292 LYS cc_start: 0.8865 (mmmt) cc_final: 0.8574 (mtmm) REVERT: C 382 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.7867 (tmm) REVERT: C 426 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7950 (tpt) REVERT: C 565 MET cc_start: 0.8037 (ppp) cc_final: 0.7439 (ptm) REVERT: C 616 MET cc_start: 0.6729 (ttt) cc_final: 0.6425 (ttt) REVERT: C 816 ARG cc_start: 0.4120 (ptt180) cc_final: 0.3836 (ptt180) REVERT: C 1036 MET cc_start: 0.7567 (mpp) cc_final: 0.7361 (mpt) REVERT: C 1048 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8324 (m-80) REVERT: D 9 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6549 (pt0) REVERT: D 90 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7366 (tm-30) REVERT: D 141 GLU cc_start: 0.8459 (tp30) cc_final: 0.7970 (tp30) REVERT: D 205 MET cc_start: 0.4439 (mmm) cc_final: 0.4000 (mmm) REVERT: D 296 LEU cc_start: 0.7297 (mt) cc_final: 0.6794 (mt) REVERT: D 320 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8475 (mt) REVERT: D 474 ARG cc_start: 0.7878 (ttp80) cc_final: 0.7553 (ttp80) REVERT: D 506 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8520 (ptt180) REVERT: D 861 ARG cc_start: 0.5339 (OUTLIER) cc_final: 0.4721 (mmt-90) REVERT: D 916 TYR cc_start: 0.7806 (m-10) cc_final: 0.7561 (m-80) REVERT: D 1006 MET cc_start: 0.2527 (ppp) cc_final: 0.1925 (ppp) REVERT: D 1076 LYS cc_start: 0.8645 (mmmt) cc_final: 0.8438 (mmmt) REVERT: D 1147 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8473 (tpp80) REVERT: E 18 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: F 245 PHE cc_start: 0.8419 (m-80) cc_final: 0.7961 (m-80) REVERT: F 278 LEU cc_start: 0.8200 (mt) cc_final: 0.7962 (mt) REVERT: F 282 ASN cc_start: 0.7089 (m-40) cc_final: 0.6843 (t0) REVERT: F 490 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8284 (tp30) REVERT: N 79 CYS cc_start: 0.3016 (OUTLIER) cc_final: 0.1837 (p) outliers start: 136 outliers final: 106 residues processed: 431 average time/residue: 0.4628 time to fit residues: 317.1769 Evaluate side-chains 431 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 315 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 597 MET Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 840 ASP Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 1024 ASP Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1104 GLU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 567 LYS Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 762 LYS Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 971 MET Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1055 LYS Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1147 ARG Chi-restraints excluded: chain D residue 1182 HIS Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 477 LYS Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 337 optimal weight: 50.0000 chunk 355 optimal weight: 30.0000 chunk 324 optimal weight: 30.0000 chunk 345 optimal weight: 10.0000 chunk 208 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 312 optimal weight: 8.9990 chunk 327 optimal weight: 50.0000 chunk 344 optimal weight: 30.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 ASN ** C 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 HIS ** C 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 416 ASN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.083 33438 Z= 0.616 Angle : 0.868 13.274 45979 Z= 0.454 Chirality : 0.051 0.314 5225 Planarity : 0.006 0.084 5422 Dihedral : 20.631 179.969 5952 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 6.28 % Allowed : 25.72 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.13), residues: 3713 helix: 0.57 (0.13), residues: 1493 sheet: -0.93 (0.23), residues: 464 loop : -1.44 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 712 HIS 0.011 0.002 HIS A 61 PHE 0.032 0.003 PHE C 892 TYR 0.024 0.003 TYR D 116 ARG 0.010 0.001 ARG C 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 298 time to evaluate : 3.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 MET cc_start: 0.8434 (ppp) cc_final: 0.7790 (ppp) REVERT: C 27 LYS cc_start: 0.7609 (mmtt) cc_final: 0.7336 (mmtt) REVERT: C 49 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8325 (mp) REVERT: C 113 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7571 (mtt90) REVERT: C 199 TRP cc_start: 0.5462 (OUTLIER) cc_final: 0.3377 (p-90) REVERT: C 202 MET cc_start: 0.7114 (mtp) cc_final: 0.6777 (mtp) REVERT: C 292 LYS cc_start: 0.9030 (mmmt) cc_final: 0.8732 (mtmm) REVERT: C 382 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7916 (tmm) REVERT: C 480 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8532 (tp) REVERT: C 565 MET cc_start: 0.8102 (ppp) cc_final: 0.7625 (ppp) REVERT: C 725 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7127 (tt0) REVERT: C 1048 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: C 1061 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7631 (tp) REVERT: C 1112 GLU cc_start: 0.7046 (tt0) cc_final: 0.6798 (tt0) REVERT: D 9 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6861 (pt0) REVERT: D 30 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8456 (mtpt) REVERT: D 59 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7032 (mt-10) REVERT: D 127 LYS cc_start: 0.6820 (mmtt) cc_final: 0.6217 (mttm) REVERT: D 141 GLU cc_start: 0.8309 (tp30) cc_final: 0.7851 (tp30) REVERT: D 296 LEU cc_start: 0.7432 (mt) cc_final: 0.6917 (mt) REVERT: D 506 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8631 (ptt180) REVERT: D 533 ASN cc_start: 0.7510 (t0) cc_final: 0.7249 (m110) REVERT: D 815 MET cc_start: 0.8821 (ptm) cc_final: 0.8396 (ptm) REVERT: D 861 ARG cc_start: 0.5841 (OUTLIER) cc_final: 0.5278 (mmp-170) REVERT: D 902 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7778 (p0) REVERT: D 910 ASP cc_start: 0.7237 (p0) cc_final: 0.6956 (p0) REVERT: E 32 TYR cc_start: 0.6500 (OUTLIER) cc_final: 0.6125 (t80) REVERT: F 245 PHE cc_start: 0.8599 (m-80) cc_final: 0.8086 (m-80) REVERT: F 282 ASN cc_start: 0.7124 (m-40) cc_final: 0.6813 (t0) REVERT: F 490 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8465 (tp30) REVERT: N 79 CYS cc_start: 0.3059 (OUTLIER) cc_final: 0.1853 (p) outliers start: 195 outliers final: 147 residues processed: 456 average time/residue: 0.4485 time to fit residues: 327.4354 Evaluate side-chains 439 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 279 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 597 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 725 GLN Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 840 ASP Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 963 ASP Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1024 ASP Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 396 ASN Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 567 LYS Chi-restraints excluded: chain D residue 625 ILE Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 792 ASN Chi-restraints excluded: chain D residue 806 MET Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 841 VAL Chi-restraints excluded: chain D residue 846 ILE Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 902 ASP Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 971 MET Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1005 THR Chi-restraints excluded: chain D residue 1055 LYS Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain D residue 1095 THR Chi-restraints excluded: chain D residue 1100 ASN Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1132 ILE Chi-restraints excluded: chain D residue 1147 ARG Chi-restraints excluded: chain D residue 1182 HIS Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1217 THR Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 415 ASP Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 477 LYS Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 227 optimal weight: 0.8980 chunk 365 optimal weight: 50.0000 chunk 223 optimal weight: 0.7980 chunk 173 optimal weight: 6.9990 chunk 254 optimal weight: 0.7980 chunk 383 optimal weight: 30.0000 chunk 353 optimal weight: 40.0000 chunk 305 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 235 optimal weight: 0.5980 chunk 187 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 ASN ** C 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 33438 Z= 0.228 Angle : 0.687 15.125 45979 Z= 0.358 Chirality : 0.044 0.334 5225 Planarity : 0.005 0.086 5422 Dihedral : 20.491 179.987 5952 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.02 % Allowed : 28.40 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3713 helix: 1.01 (0.13), residues: 1496 sheet: -0.68 (0.25), residues: 435 loop : -1.26 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 930 HIS 0.005 0.001 HIS F 354 PHE 0.034 0.002 PHE F 245 TYR 0.029 0.002 TYR E 32 ARG 0.010 0.001 ARG D1146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 299 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7545 (p0) cc_final: 0.7199 (p0) REVERT: C 27 LYS cc_start: 0.7439 (mmtt) cc_final: 0.7183 (mmtt) REVERT: C 49 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8190 (mp) REVERT: C 113 ARG cc_start: 0.7758 (mtm-85) cc_final: 0.7475 (mtt90) REVERT: C 202 MET cc_start: 0.6798 (mtp) cc_final: 0.6499 (mtp) REVERT: C 243 TYR cc_start: 0.8077 (m-80) cc_final: 0.7622 (m-80) REVERT: C 292 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8723 (mtmm) REVERT: C 382 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7927 (tmm) REVERT: C 534 LEU cc_start: 0.8658 (tt) cc_final: 0.8379 (mp) REVERT: C 565 MET cc_start: 0.7912 (ppp) cc_final: 0.7295 (ptm) REVERT: C 808 ARG cc_start: 0.7768 (ptp-170) cc_final: 0.7275 (mtt180) REVERT: C 1048 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.8322 (m-80) REVERT: D 9 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6546 (pt0) REVERT: D 30 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8314 (mtpt) REVERT: D 59 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6864 (mt-10) REVERT: D 127 LYS cc_start: 0.6802 (mmtt) cc_final: 0.6241 (mttm) REVERT: D 141 GLU cc_start: 0.8337 (tp30) cc_final: 0.7893 (tp30) REVERT: D 205 MET cc_start: 0.4531 (mmm) cc_final: 0.4097 (mmm) REVERT: D 296 LEU cc_start: 0.7310 (mt) cc_final: 0.6853 (mt) REVERT: D 320 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8469 (mt) REVERT: D 506 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8579 (ptt180) REVERT: D 861 ARG cc_start: 0.5472 (OUTLIER) cc_final: 0.4931 (mmt-90) REVERT: D 902 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7742 (p0) REVERT: D 910 ASP cc_start: 0.7548 (p0) cc_final: 0.7110 (p0) REVERT: D 1006 MET cc_start: 0.2519 (ppp) cc_final: 0.1941 (ppp) REVERT: D 1031 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8532 (mm-30) REVERT: D 1147 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8414 (tpp80) REVERT: F 245 PHE cc_start: 0.8475 (m-80) cc_final: 0.7967 (m-80) REVERT: F 490 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8386 (tp30) REVERT: N 79 CYS cc_start: 0.3050 (OUTLIER) cc_final: 0.1882 (p) outliers start: 125 outliers final: 101 residues processed: 399 average time/residue: 0.4935 time to fit residues: 313.6935 Evaluate side-chains 401 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 290 time to evaluate : 3.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 597 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain C residue 840 ASP Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1024 ASP Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 762 LYS Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 902 ASP Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 971 MET Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1100 ASN Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1132 ILE Chi-restraints excluded: chain D residue 1147 ARG Chi-restraints excluded: chain D residue 1182 HIS Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 415 ASP Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 242 optimal weight: 0.6980 chunk 325 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 281 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 305 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 chunk 314 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.173650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.128712 restraints weight = 64998.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.124206 restraints weight = 72531.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.126047 restraints weight = 72579.592| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33438 Z= 0.236 Angle : 0.684 14.861 45979 Z= 0.355 Chirality : 0.043 0.344 5225 Planarity : 0.005 0.061 5422 Dihedral : 20.445 179.796 5952 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.38 % Allowed : 28.17 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.14), residues: 3713 helix: 1.10 (0.13), residues: 1498 sheet: -0.62 (0.25), residues: 445 loop : -1.19 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 718 HIS 0.005 0.001 HIS F 354 PHE 0.033 0.001 PHE F 245 TYR 0.031 0.002 TYR E 32 ARG 0.014 0.000 ARG D 474 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6992.36 seconds wall clock time: 128 minutes 33.68 seconds (7713.68 seconds total)