Starting phenix.real_space_refine on Fri Feb 23 03:07:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7k_13238/02_2024/7p7k_13238_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7k_13238/02_2024/7p7k_13238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7k_13238/02_2024/7p7k_13238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7k_13238/02_2024/7p7k_13238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7k_13238/02_2024/7p7k_13238_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7k_13238/02_2024/7p7k_13238_updated.pdb" } resolution = 3.1 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= 0.005 sd= 0.019 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 Ca 1 9.91 5 Fe 32 7.16 5 P 9 5.49 5 S 263 5.16 5 C 23789 2.51 5 N 6029 2.21 5 O 6408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36531 Number of models: 1 Model: "" Number of chains: 23 Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7022 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4575 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 533} Chain breaks: 3 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1330 Classifications: {'peptide': 168} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 156} Chain breaks: 2 Chain: "I" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1185 Classifications: {'peptide': 149} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 135} Chain: "H" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2334 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 285} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 808 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 1 Chain: "L" Number of atoms: 4548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4548 Classifications: {'peptide': 599} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 580} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 482} Chain: "N" Number of atoms: 3620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3620 Classifications: {'peptide': 478} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 457} Chain breaks: 1 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1210 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 156} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "L" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 159 Unusual residues: {'3PE': 3, 'LFA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "M" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'LFA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 70.538 58.904 201.172 1.00 28.99 S ATOM 2741 SG CYS F 357 74.005 58.437 205.554 1.00 43.17 S ATOM 3062 SG CYS F 398 68.353 54.803 205.881 1.00 42.91 S ATOM 2697 SG CYS F 351 72.964 52.636 202.267 1.00 37.56 S ATOM 4054 SG CYS E 92 81.619 50.445 221.840 1.00 59.56 S ATOM 4088 SG CYS E 97 81.816 51.160 225.339 1.00 68.83 S ATOM 4366 SG CYS E 133 76.505 49.633 221.578 1.00 71.18 S ATOM 4392 SG CYS E 137 75.627 50.243 224.764 1.00 65.94 S ATOM 5476 SG CYS G 114 80.757 65.791 183.843 1.00 24.10 S ATOM 5416 SG CYS G 105 85.811 69.990 185.414 1.00 29.22 S ATOM 5436 SG CYS G 108 86.771 64.122 182.991 1.00 25.62 S ATOM 5830 SG CYS G 156 75.340 57.687 188.612 1.00 21.94 S ATOM 5811 SG CYS G 153 81.237 56.857 191.543 1.00 22.70 S ATOM 5859 SG CYS G 159 78.620 52.186 187.920 1.00 19.92 S ATOM 6203 SG CYS G 203 80.491 57.535 184.915 1.00 12.85 S ATOM 6428 SG CYS G 230 77.580 49.451 163.675 1.00 19.08 S ATOM 6713 SG CYS G 265 77.761 45.572 168.945 1.00 19.36 S ATOM 6476 SG CYS G 237 72.273 48.795 166.730 1.00 17.83 S ATOM 6452 SG CYS G 233 74.822 43.606 163.652 1.00 19.24 S ATOM 4877 SG CYS G 36 68.883 58.298 191.250 1.00 24.33 S ATOM 4953 SG CYS G 47 70.340 61.611 191.813 1.00 22.94 S ATOM 4979 SG CYS G 50 64.438 63.051 191.738 1.00 34.28 S ATOM 5128 SG CYS G 69 64.164 59.419 191.183 1.00 29.03 S ATOM 16871 SG CYS B 129 89.711 94.343 160.263 1.00 39.78 S ATOM 16434 SG CYS B 64 94.680 98.365 162.055 1.00 64.15 S ATOM 16428 SG CYS B 63 89.031 99.912 164.071 1.00 62.31 S ATOM 17088 SG CYS B 158 91.632 94.189 166.081 1.00 71.00 S ATOM 18129 SG CYS I 102 90.348 88.169 172.013 1.00 17.46 S ATOM 18104 SG CYS I 99 95.978 87.161 168.467 1.00 11.91 S ATOM 18147 SG CYS I 105 94.601 83.745 173.771 1.00 28.17 S ATOM 17862 SG CYS I 70 90.800 82.960 168.579 1.00 15.21 S ATOM 18176 SG CYS I 109 95.943 78.155 180.014 1.00 17.05 S ATOM 17839 SG CYS I 66 94.015 77.502 173.877 1.00 12.17 S ATOM 17799 SG CYS I 60 98.342 73.416 175.968 1.00 21.62 S ATOM 17817 SG CYS I 63 92.113 73.453 178.604 1.00 10.39 S Time building chain proxies: 18.98, per 1000 atoms: 0.52 Number of scatterers: 36531 At special positions: 0 Unit cell: (154.76, 208.82, 252.28, 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) Fe 32 26.01 Ca 1 19.99 S 263 16.00 P 9 15.00 O 6408 8.00 N 6029 7.00 C 23789 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: 13.81 Conformation dependent library (CDL) restraints added in 7.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb=" SF4 G1003 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " Number of angles added : 93 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8460 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 191 helices and 26 sheets defined 54.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.26 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 56 Processing helix chain 'F' and resid 69 through 75 Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 178 through 181 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 219 through 231 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 270 through 276 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 311 through 316 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 355 through 372 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 421 Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.871A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.714A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG E 47 " --> pdb=" O GLN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.059A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 158 through 162 Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 115 through 122 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 196 through 202 Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 220 through 222 No H-bonds generated for 'chain 'G' and resid 220 through 222' Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 273 through 276 Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 370 through 373 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 410 removed outlier: 4.549A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN G 410 " --> pdb=" O MET G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 423 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 509 through 524 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 560 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 601 through 604 removed outlier: 3.530A pdb=" N GLU G 604 " --> pdb=" O ALA G 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 601 through 604' Processing helix chain 'G' and resid 615 through 617 No H-bonds generated for 'chain 'G' and resid 615 through 617' Processing helix chain 'G' and resid 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 689 removed outlier: 4.669A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 764 through 770 Processing helix chain 'G' and resid 825 through 829 Processing helix chain 'G' and resid 831 through 834 No H-bonds generated for 'chain 'G' and resid 831 through 834' Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'G' and resid 895 through 897 No H-bonds generated for 'chain 'G' and resid 895 through 897' Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 57 through 66 Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.906A pdb=" N TRP C 136 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE C 145 " --> pdb=" O TRP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 280 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 328 Processing helix chain 'C' and resid 342 through 353 Processing helix chain 'C' and resid 376 through 384 Processing helix chain 'C' and resid 387 through 399 Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 431 Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 523 Processing helix chain 'C' and resid 564 through 570 Processing helix chain 'C' and resid 572 through 574 No H-bonds generated for 'chain 'C' and resid 572 through 574' Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 40 through 51 Processing helix chain 'B' and resid 63 through 72 removed outlier: 3.653A pdb=" N PHE B 72 " --> pdb=" O MET B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 162 through 178 Processing helix chain 'B' and resid 200 through 203 No H-bonds generated for 'chain 'B' and resid 200 through 203' Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 127 through 130 Processing helix chain 'I' and resid 134 through 137 No H-bonds generated for 'chain 'I' and resid 134 through 137' Processing helix chain 'I' and resid 150 through 152 No H-bonds generated for 'chain 'I' and resid 150 through 152' Processing helix chain 'H' and resid 6 through 39 Processing helix chain 'H' and resid 57 through 69 Processing helix chain 'H' and resid 81 through 100 Proline residue: H 87 - end of helix removed outlier: 4.898A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 137 removed outlier: 4.716A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 157 Processing helix chain 'H' and resid 160 through 171 removed outlier: 4.315A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'H' and resid 188 through 191 No H-bonds generated for 'chain 'H' and resid 188 through 191' Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 232 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 303 Processing helix chain 'H' and resid 305 through 323 Processing helix chain 'A' and resid 8 through 36 Processing helix chain 'A' and resid 67 through 119 removed outlier: 3.771A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 20 removed outlier: 4.312A pdb=" N ALA L 5 " --> pdb=" O ASN L 2 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR L 7 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU L 10 " --> pdb=" O THR L 7 " (cutoff:3.500A) Proline residue: L 11 - end of helix removed outlier: 3.502A pdb=" N LEU L 17 " --> pdb=" O GLY L 14 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE L 20 " --> pdb=" O LEU L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 54 Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 132 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 214 through 229 Processing helix chain 'L' and resid 238 through 244 removed outlier: 4.837A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 254 Processing helix chain 'L' and resid 261 through 268 Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 277 through 299 removed outlier: 3.629A pdb=" N LEU L 299 " --> pdb=" O GLY L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 356 Processing helix chain 'L' and resid 368 through 371 No H-bonds generated for 'chain 'L' and resid 368 through 371' Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 412 through 436 Processing helix chain 'L' and resid 455 through 464 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 538 through 560 removed outlier: 6.100A pdb=" N ASP L 542 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE L 549 " --> pdb=" O ASP L 546 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N VAL L 550 " --> pdb=" O LYS L 547 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LYS L 551 " --> pdb=" O VAL L 548 " (cutoff:3.500A) Proline residue: L 552 - end of helix removed outlier: 3.542A pdb=" N LEU L 560 " --> pdb=" O ALA L 557 " (cutoff:3.500A) Processing helix chain 'L' and resid 564 through 586 Proline residue: L 572 - end of helix removed outlier: 3.751A pdb=" N LEU L 585 " --> pdb=" O LYS L 581 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER L 586 " --> pdb=" O GLY L 582 " (cutoff:3.500A) Processing helix chain 'L' and resid 591 through 611 Processing helix chain 'M' and resid 3 through 23 Proline residue: M 10 - end of helix removed outlier: 3.719A pdb=" N GLU M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ARG M 22 " --> pdb=" O TRP M 18 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N PHE M 23 " --> pdb=" O GLN M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 50 Processing helix chain 'M' and resid 85 through 105 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 156 removed outlier: 3.638A pdb=" N MET M 146 " --> pdb=" O PHE M 142 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Proline residue: M 149 - end of helix Processing helix chain 'M' and resid 164 through 199 Processing helix chain 'M' and resid 219 through 233 Processing helix chain 'M' and resid 242 through 249 removed outlier: 3.950A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 266 through 278 removed outlier: 4.648A pdb=" N LEU M 276 " --> pdb=" O LEU M 272 " (cutoff:3.500A) Proline residue: M 277 - end of helix Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 332 removed outlier: 3.757A pdb=" N TYR M 331 " --> pdb=" O LEU M 327 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR M 332 " --> pdb=" O ILE M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 371 through 373 No H-bonds generated for 'chain 'M' and resid 371 through 373' Processing helix chain 'M' and resid 384 through 395 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 502 removed outlier: 4.822A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA M 492 " --> pdb=" O THR M 488 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 34 through 58 removed outlier: 4.496A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.204A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 120 Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 181 Processing helix chain 'N' and resid 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 226 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.448A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 286 Processing helix chain 'N' and resid 294 through 316 removed outlier: 3.713A pdb=" N ALA N 315 " --> pdb=" O VAL N 311 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU N 316 " --> pdb=" O ALA N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 322 through 347 Processing helix chain 'N' and resid 365 through 367 No H-bonds generated for 'chain 'N' and resid 365 through 367' Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 432 Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 479 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 53 Processing helix chain 'K' and resid 57 through 87 Processing helix chain 'J' and resid 2 through 21 removed outlier: 3.575A pdb=" N THR J 21 " --> pdb=" O LEU J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 46 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 86 through 88 No H-bonds generated for 'chain 'J' and resid 86 through 88' Processing helix chain 'J' and resid 90 through 113 removed outlier: 5.517A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix removed outlier: 3.724A pdb=" N GLY J 113 " --> pdb=" O TYR J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 158 Processing sheet with id= A, first strand: chain 'F' and resid 214 through 218 removed outlier: 6.719A pdb=" N TYR F 86 " --> pdb=" O CYS F 215 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN F 217 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU F 88 " --> pdb=" O ASN F 217 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N HIS F 172 " --> pdb=" O LEU F 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'F' and resid 247 through 250 Processing sheet with id= C, first strand: chain 'F' and resid 251 through 253 Processing sheet with id= D, first strand: chain 'E' and resid 87 through 92 Processing sheet with id= E, first strand: chain 'E' and resid 143 through 145 Processing sheet with id= F, first strand: chain 'G' and resid 11 through 14 removed outlier: 6.626A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N PHE G 78 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= H, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= I, first strand: chain 'G' and resid 224 through 229 removed outlier: 6.471A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 284 through 288 Processing sheet with id= K, first strand: chain 'G' and resid 314 through 317 removed outlier: 6.546A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU G 610 " --> pdb=" O ASP G 596 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 530 through 534 removed outlier: 6.333A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL G 379 " --> pdb=" O PRO G 430 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE G 432 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N TYR G 449 " --> pdb=" O ASN G 435 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 620 through 623 Processing sheet with id= N, first strand: chain 'G' and resid 813 through 817 Processing sheet with id= O, first strand: chain 'G' and resid 841 through 844 removed outlier: 7.983A pdb=" N ILE G 842 " --> pdb=" O THR G 870 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU G 844 " --> pdb=" O PRO G 872 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU G 874 " --> pdb=" O LEU G 844 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.188A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LEU C 74 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.480A pdb=" N THR C 148 " --> pdb=" O VAL C 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 216 through 219 removed outlier: 3.713A pdb=" N ARG C 232 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ILE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 531 through 538 Processing sheet with id= T, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.435A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL B 153 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'I' and resid 48 through 50 Processing sheet with id= V, first strand: chain 'I' and resid 75 through 81 removed outlier: 3.983A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 68 through 70 Processing sheet with id= X, first strand: chain 'L' and resid 60 through 66 removed outlier: 6.860A pdb=" N PHE L 77 " --> pdb=" O LEU L 64 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.848A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'N' and resid 61 through 63 1825 hydrogen bonds defined for protein. 5220 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.48 Time building geometry restraints manager: 15.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 15545 1.42 - 1.64: 21400 1.64 - 1.86: 401 1.86 - 2.09: 0 2.09 - 2.31: 92 Bond restraints: 37438 Sorted by residual: bond pdb=" O13 3PE H 602 " pdb=" P 3PE H 602 " ideal model delta sigma weight residual 1.654 1.592 0.062 2.00e-02 2.50e+03 9.52e+00 bond pdb=" O13 3PE A 201 " pdb=" P 3PE A 201 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 9.02e+00 bond pdb=" O13 3PE M1002 " pdb=" P 3PE M1002 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 8.97e+00 bond pdb=" O13 3PE M1003 " pdb=" P 3PE M1003 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 8.87e+00 bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.82e+00 ... (remaining 37433 not shown) Histogram of bond angle deviations from ideal: 69.08 - 82.51: 88 82.51 - 95.93: 1 95.93 - 109.36: 3562 109.36 - 122.79: 44435 122.79 - 136.22: 2706 Bond angle restraints: 50792 Sorted by residual: angle pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta sigma weight residual 121.80 133.47 -11.67 2.44e+00 1.68e-01 2.29e+01 angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 99.59 10.22 2.21e+00 2.05e-01 2.14e+01 angle pdb=" C ALA G 177 " pdb=" N HIS G 178 " pdb=" CA HIS G 178 " ideal model delta sigma weight residual 121.54 130.26 -8.72 1.91e+00 2.74e-01 2.08e+01 angle pdb=" S3 SF4 F 501 " pdb="FE1 SF4 F 501 " pdb=" S4 SF4 F 501 " ideal model delta sigma weight residual 104.10 110.14 -6.04 1.50e+00 4.44e-01 1.62e+01 angle pdb=" N MET C 387 " pdb=" CA MET C 387 " pdb=" C MET C 387 " ideal model delta sigma weight residual 109.81 118.71 -8.90 2.21e+00 2.05e-01 1.62e+01 ... (remaining 50787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.98: 21616 33.98 - 67.95: 380 67.95 - 101.93: 23 101.93 - 135.91: 6 135.91 - 169.88: 1 Dihedral angle restraints: 22026 sinusoidal: 8802 harmonic: 13224 Sorted by residual: dihedral pdb=" CA HIS H 210 " pdb=" C HIS H 210 " pdb=" N PRO H 211 " pdb=" CA PRO H 211 " ideal model delta harmonic sigma weight residual 180.00 130.20 49.80 0 5.00e+00 4.00e-02 9.92e+01 dihedral pdb=" CA VAL N 63 " pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta harmonic sigma weight residual 180.00 135.99 44.01 0 5.00e+00 4.00e-02 7.75e+01 dihedral pdb=" CA ASN G 260 " pdb=" C ASN G 260 " pdb=" N HIS G 261 " pdb=" CA HIS G 261 " ideal model delta harmonic sigma weight residual 180.00 -144.85 -35.15 0 5.00e+00 4.00e-02 4.94e+01 ... (remaining 22023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.236: 5655 4.236 - 8.471: 0 8.471 - 12.707: 0 12.707 - 16.942: 0 16.942 - 21.178: 28 Chirality restraints: 5683 Sorted by residual: chirality pdb="FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.62 -21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 G1002 " pdb=" S1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " both_signs ideal model delta sigma weight residual False 10.55 -10.60 21.16 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE2 SF4 B 301 " pdb=" S1 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.60 21.15 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5680 not shown) Planarity restraints: 6349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.019 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C VAL N 63 " 0.064 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.024 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS H 210 " 0.056 5.00e-02 4.00e+02 8.48e-02 1.15e+01 pdb=" N PRO H 211 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO H 211 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO H 211 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 212 " 0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO F 213 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO F 213 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 213 " 0.040 5.00e-02 4.00e+02 ... (remaining 6346 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 7363 2.77 - 3.30: 34392 3.30 - 3.84: 66188 3.84 - 4.37: 80180 4.37 - 4.90: 135230 Nonbonded interactions: 323353 Sorted by model distance: nonbonded pdb=" OG1 THR I 82 " pdb=" OD1 ASP I 84 " model vdw 2.238 2.440 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.243 2.440 nonbonded pdb=" OH TYR L 318 " pdb=" O GLY L 418 " model vdw 2.248 2.440 nonbonded pdb=" OE2 GLU N 324 " pdb=" OH TYR N 397 " model vdw 2.268 2.440 nonbonded pdb=" OH TYR G 255 " pdb=" O GLY G 776 " model vdw 2.272 2.440 ... (remaining 323348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 3.910 Check model and map are aligned: 0.630 Set scattering table: 0.320 Process input model: 103.220 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.120 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 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 : 0.006 0.082 37438 Z= 0.402 Angle : 0.709 11.669 50792 Z= 0.373 Chirality : 1.482 21.178 5683 Planarity : 0.006 0.085 6349 Dihedral : 13.055 169.882 13566 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.51 % Favored : 97.47 % Rotamer: Outliers : 2.21 % Allowed : 5.64 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.05 % 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: -0.42 (0.11), residues: 4584 helix: 0.28 (0.09), residues: 2660 sheet: -0.66 (0.28), residues: 302 loop : -0.98 (0.14), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP M 47 HIS 0.009 0.001 HIS G 101 PHE 0.041 0.002 PHE L 341 TYR 0.031 0.002 TYR L 428 ARG 0.007 0.001 ARG G 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 603 time to evaluate : 4.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 238 ASN cc_start: 0.8863 (m-40) cc_final: 0.8595 (m-40) REVERT: F 250 MET cc_start: 0.9154 (mtt) cc_final: 0.8942 (mtt) REVERT: F 387 LEU cc_start: 0.9165 (tp) cc_final: 0.8852 (mt) REVERT: E 19 ARG cc_start: 0.8770 (ttm-80) cc_final: 0.8567 (ttp-170) REVERT: E 112 LYS cc_start: 0.8440 (tptm) cc_final: 0.8221 (tptt) REVERT: E 114 ASN cc_start: 0.9094 (t0) cc_final: 0.8878 (t0) REVERT: G 233 CYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8371 (p) REVERT: G 405 GLU cc_start: 0.8850 (tt0) cc_final: 0.8566 (pt0) REVERT: G 854 VAL cc_start: 0.8813 (t) cc_final: 0.8552 (m) REVERT: G 862 PHE cc_start: 0.9271 (p90) cc_final: 0.9006 (p90) REVERT: G 896 VAL cc_start: 0.9240 (p) cc_final: 0.8915 (m) REVERT: G 901 HIS cc_start: 0.8490 (p90) cc_final: 0.8062 (p-80) REVERT: C 36 ASP cc_start: 0.8777 (p0) cc_final: 0.8510 (p0) REVERT: C 204 TRP cc_start: 0.8439 (m100) cc_final: 0.8190 (m100) REVERT: C 595 MET cc_start: 0.9224 (tpt) cc_final: 0.8974 (mmm) REVERT: I 55 ASP cc_start: 0.8718 (m-30) cc_final: 0.8372 (m-30) REVERT: I 147 GLU cc_start: 0.8862 (mp0) cc_final: 0.8248 (pp20) REVERT: I 153 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.6714 (mmt) REVERT: H 27 THR cc_start: 0.8606 (m) cc_final: 0.8364 (p) REVERT: H 37 ARG cc_start: 0.7678 (ttm170) cc_final: 0.7313 (ttt180) REVERT: H 152 GLN cc_start: 0.8623 (tt0) cc_final: 0.8380 (tt0) REVERT: H 229 TYR cc_start: 0.8464 (m-80) cc_final: 0.7996 (m-80) REVERT: H 285 ILE cc_start: 0.9050 (mm) cc_final: 0.8819 (mm) REVERT: H 296 GLN cc_start: 0.8784 (mt0) cc_final: 0.8505 (mt0) REVERT: H 298 MET cc_start: 0.8728 (mmp) cc_final: 0.8455 (mmp) REVERT: L 77 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8444 (m-80) REVERT: L 105 TRP cc_start: 0.8350 (t60) cc_final: 0.7508 (m100) REVERT: L 365 MET cc_start: 0.7868 (mpp) cc_final: 0.7103 (mtm) REVERT: L 424 MET cc_start: 0.8535 (mtp) cc_final: 0.8333 (mtm) REVERT: M 20 THR cc_start: 0.9137 (t) cc_final: 0.8921 (t) REVERT: M 224 MET cc_start: 0.8999 (tmm) cc_final: 0.8465 (tmm) REVERT: M 291 MET cc_start: 0.9019 (mtm) cc_final: 0.8794 (mtm) REVERT: N 1 MET cc_start: 0.6935 (mtp) cc_final: 0.5622 (ttp) REVERT: N 72 PHE cc_start: 0.9065 (t80) cc_final: 0.8847 (t80) REVERT: K 99 ARG cc_start: 0.8176 (ptp-170) cc_final: 0.7941 (ptp90) REVERT: J 55 GLU cc_start: 0.9003 (tp30) cc_final: 0.8680 (tp30) outliers start: 83 outliers final: 26 residues processed: 660 average time/residue: 0.5455 time to fit residues: 577.7503 Evaluate side-chains 498 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 469 time to evaluate : 4.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 233 CYS Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain J residue 23 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 385 optimal weight: 10.0000 chunk 345 optimal weight: 3.9990 chunk 191 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 233 optimal weight: 0.0040 chunk 184 optimal weight: 8.9990 chunk 357 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 217 optimal weight: 9.9990 chunk 266 optimal weight: 10.0000 chunk 414 optimal weight: 7.9990 overall best weight: 4.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 11 HIS F 22 GLN F 53 GLN F 237 GLN F 425 GLN E 44 GLN E 106 GLN G 20 ASN G 238 ASN G 583 ASN G 808 GLN G 883 GLN C 359 HIS B 47 ASN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN N 404 GLN K 82 GLN ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.249 37438 Z= 0.799 Angle : 2.206 50.793 50792 Z= 1.451 Chirality : 0.446 6.474 5683 Planarity : 0.005 0.068 6349 Dihedral : 9.229 169.691 5486 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.14 % Favored : 97.84 % Rotamer: Outliers : 1.81 % Allowed : 8.41 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % 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: 0.44 (0.12), residues: 4584 helix: 1.08 (0.10), residues: 2638 sheet: -0.55 (0.29), residues: 296 loop : -0.76 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP M 47 HIS 0.008 0.001 HIS G 178 PHE 0.029 0.002 PHE L 341 TYR 0.022 0.002 TYR L 428 ARG 0.006 0.000 ARG C 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 492 time to evaluate : 4.337 Fit side-chains revert: symmetry clash REVERT: F 250 MET cc_start: 0.9159 (mtt) cc_final: 0.8950 (mtt) REVERT: E 114 ASN cc_start: 0.9118 (t0) cc_final: 0.8771 (t0) REVERT: G 56 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8926 (mm-40) REVERT: G 405 GLU cc_start: 0.8787 (tt0) cc_final: 0.8523 (pt0) REVERT: G 896 VAL cc_start: 0.9212 (p) cc_final: 0.8891 (m) REVERT: G 901 HIS cc_start: 0.8577 (p90) cc_final: 0.8175 (p-80) REVERT: C 36 ASP cc_start: 0.8770 (p0) cc_final: 0.8507 (p0) REVERT: C 243 VAL cc_start: 0.9371 (OUTLIER) cc_final: 0.9028 (p) REVERT: C 488 MET cc_start: 0.8336 (tpt) cc_final: 0.7598 (tpt) REVERT: C 597 ASP cc_start: 0.9064 (t0) cc_final: 0.8788 (t70) REVERT: I 147 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8482 (mp0) REVERT: H 152 GLN cc_start: 0.8593 (tt0) cc_final: 0.8358 (tt0) REVERT: H 214 GLN cc_start: 0.4914 (pt0) cc_final: 0.4631 (mp10) REVERT: H 229 TYR cc_start: 0.8425 (m-80) cc_final: 0.7915 (m-80) REVERT: H 285 ILE cc_start: 0.9077 (mm) cc_final: 0.8826 (mm) REVERT: H 298 MET cc_start: 0.8754 (mmp) cc_final: 0.8468 (mmp) REVERT: H 322 TRP cc_start: 0.8143 (t60) cc_final: 0.7717 (t-100) REVERT: L 77 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8517 (m-80) REVERT: L 105 TRP cc_start: 0.8289 (t60) cc_final: 0.7444 (m100) REVERT: L 150 SER cc_start: 0.9347 (t) cc_final: 0.8934 (m) REVERT: L 487 HIS cc_start: 0.7451 (t70) cc_final: 0.7090 (t70) REVERT: M 224 MET cc_start: 0.8911 (tmm) cc_final: 0.8698 (tmm) REVERT: N 1 MET cc_start: 0.6931 (mtp) cc_final: 0.5592 (ttp) REVERT: N 57 GLN cc_start: 0.8706 (mm110) cc_final: 0.8388 (mm110) REVERT: K 99 ARG cc_start: 0.8219 (ptp-170) cc_final: 0.7955 (ptp90) REVERT: J 94 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8434 (mm) outliers start: 68 outliers final: 44 residues processed: 543 average time/residue: 0.5187 time to fit residues: 450.8202 Evaluate side-chains 509 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 460 time to evaluate : 4.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 261 HIS Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 721 ILE Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 94 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 230 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 344 optimal weight: 10.0000 chunk 281 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 414 optimal weight: 8.9990 chunk 448 optimal weight: 9.9990 chunk 369 optimal weight: 0.9990 chunk 411 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 332 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 GLN F 304 HIS F 425 GLN E 106 GLN E 119 GLN G 238 ASN B 47 ASN ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 261 GLN H 296 GLN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN ** N 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN J 24 ASN J 115 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 37438 Z= 0.785 Angle : 2.201 50.651 50792 Z= 1.448 Chirality : 0.450 6.498 5683 Planarity : 0.005 0.067 6349 Dihedral : 9.059 169.006 5468 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.38 % Favored : 97.60 % Rotamer: Outliers : 2.58 % Allowed : 8.75 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % 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: 0.83 (0.12), residues: 4584 helix: 1.41 (0.10), residues: 2634 sheet: -0.39 (0.30), residues: 291 loop : -0.60 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP M 47 HIS 0.009 0.001 HIS G 178 PHE 0.027 0.002 PHE L 341 TYR 0.022 0.002 TYR L 428 ARG 0.007 0.000 ARG G 664 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 467 time to evaluate : 4.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 114 ASN cc_start: 0.9106 (t0) cc_final: 0.8902 (t0) REVERT: G 56 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8903 (mm-40) REVERT: G 405 GLU cc_start: 0.8769 (tt0) cc_final: 0.8508 (pt0) REVERT: G 901 HIS cc_start: 0.8632 (p90) cc_final: 0.8160 (p-80) REVERT: C 36 ASP cc_start: 0.8762 (p0) cc_final: 0.8540 (p0) REVERT: C 488 MET cc_start: 0.8287 (tpt) cc_final: 0.7559 (tpt) REVERT: I 147 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8483 (mp0) REVERT: I 153 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6537 (mmt) REVERT: H 152 GLN cc_start: 0.8661 (tt0) cc_final: 0.8415 (tt0) REVERT: H 214 GLN cc_start: 0.4940 (pt0) cc_final: 0.4668 (mp10) REVERT: H 228 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8516 (tt0) REVERT: H 285 ILE cc_start: 0.9072 (mm) cc_final: 0.8832 (mm) REVERT: H 296 GLN cc_start: 0.8726 (mt0) cc_final: 0.8523 (mt0) REVERT: H 298 MET cc_start: 0.8713 (mmp) cc_final: 0.8414 (mmp) REVERT: H 322 TRP cc_start: 0.8207 (t60) cc_final: 0.7808 (t-100) REVERT: A 36 PHE cc_start: 0.8380 (t80) cc_final: 0.8171 (t80) REVERT: L 77 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8552 (m-80) REVERT: L 105 TRP cc_start: 0.8307 (t60) cc_final: 0.7504 (m-10) REVERT: L 127 MET cc_start: 0.9081 (tpt) cc_final: 0.8875 (tpt) REVERT: M 224 MET cc_start: 0.8984 (tmm) cc_final: 0.8256 (tmm) REVERT: N 1 MET cc_start: 0.6964 (mtp) cc_final: 0.5644 (ttp) REVERT: N 57 GLN cc_start: 0.8767 (mm110) cc_final: 0.8384 (mm110) REVERT: K 99 ARG cc_start: 0.8190 (ptp-170) cc_final: 0.7913 (ptp90) REVERT: J 64 MET cc_start: 0.9181 (mmp) cc_final: 0.8861 (mmp) REVERT: J 94 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8498 (mm) REVERT: J 116 ASP cc_start: 0.8839 (t0) cc_final: 0.8534 (t0) outliers start: 97 outliers final: 56 residues processed: 539 average time/residue: 0.5171 time to fit residues: 451.2839 Evaluate side-chains 514 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 453 time to evaluate : 4.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 261 HIS Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 721 ILE Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 409 optimal weight: 1.9990 chunk 311 optimal weight: 0.0870 chunk 215 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 278 optimal weight: 5.9990 chunk 416 optimal weight: 8.9990 chunk 440 optimal weight: 1.9990 chunk 217 optimal weight: 8.9990 chunk 394 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 GLN F 425 GLN E 106 GLN E 119 GLN G 238 ASN G 490 GLN B 47 ASN H 175 ASN ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN N 317 GLN N 404 GLN J 24 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 37438 Z= 0.764 Angle : 2.194 50.609 50792 Z= 1.446 Chirality : 0.447 6.435 5683 Planarity : 0.004 0.067 6349 Dihedral : 8.881 168.513 5464 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.18 % Favored : 97.80 % Rotamer: Outliers : 2.15 % Allowed : 9.76 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % 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: 1.06 (0.12), residues: 4584 helix: 1.64 (0.10), residues: 2620 sheet: -0.39 (0.29), residues: 298 loop : -0.55 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M 47 HIS 0.008 0.001 HIS G 178 PHE 0.027 0.001 PHE L 341 TYR 0.021 0.001 TYR N 424 ARG 0.006 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 466 time to evaluate : 4.668 Fit side-chains revert: symmetry clash REVERT: E 114 ASN cc_start: 0.9079 (t0) cc_final: 0.8877 (t0) REVERT: G 56 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8911 (mm-40) REVERT: G 405 GLU cc_start: 0.8725 (tt0) cc_final: 0.8486 (pt0) REVERT: G 617 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8494 (mp0) REVERT: G 901 HIS cc_start: 0.8637 (p90) cc_final: 0.8178 (p-80) REVERT: C 36 ASP cc_start: 0.8755 (p0) cc_final: 0.8535 (p0) REVERT: C 597 ASP cc_start: 0.8964 (t0) cc_final: 0.8528 (t70) REVERT: I 147 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8488 (mp0) REVERT: I 153 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6521 (mmt) REVERT: H 32 MET cc_start: 0.2863 (mtt) cc_final: 0.2592 (mtt) REVERT: H 152 GLN cc_start: 0.8580 (tt0) cc_final: 0.8357 (tt0) REVERT: H 228 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8484 (tt0) REVERT: H 285 ILE cc_start: 0.9047 (mm) cc_final: 0.8821 (mm) REVERT: H 298 MET cc_start: 0.8690 (mmp) cc_final: 0.8404 (mmp) REVERT: H 322 TRP cc_start: 0.8203 (t60) cc_final: 0.7776 (t-100) REVERT: A 36 PHE cc_start: 0.8394 (t80) cc_final: 0.8084 (t80) REVERT: L 77 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8496 (m-80) REVERT: L 105 TRP cc_start: 0.8281 (t60) cc_final: 0.7460 (m-10) REVERT: L 127 MET cc_start: 0.9079 (tpt) cc_final: 0.8844 (tpt) REVERT: M 224 MET cc_start: 0.8894 (tmm) cc_final: 0.8195 (tmm) REVERT: M 429 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7856 (tt) REVERT: N 1 MET cc_start: 0.6964 (mtp) cc_final: 0.5660 (ttp) REVERT: K 99 ARG cc_start: 0.8190 (ptp-170) cc_final: 0.7920 (ptp90) REVERT: J 94 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8520 (mt) outliers start: 81 outliers final: 54 residues processed: 521 average time/residue: 0.5119 time to fit residues: 429.6842 Evaluate side-chains 511 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 450 time to evaluate : 4.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 261 HIS Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 721 ILE Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 367 optimal weight: 1.9990 chunk 250 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 328 optimal weight: 8.9990 chunk 181 optimal weight: 0.9990 chunk 376 optimal weight: 5.9990 chunk 304 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 225 optimal weight: 0.9990 chunk 395 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN E 106 GLN E 119 GLN G 238 ASN G 352 GLN G 490 GLN G 808 GLN B 47 ASN ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN N 149 GLN N 232 GLN N 317 GLN N 404 GLN J 24 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 37438 Z= 0.766 Angle : 2.194 50.617 50792 Z= 1.446 Chirality : 0.447 6.436 5683 Planarity : 0.004 0.066 6349 Dihedral : 8.823 168.127 5464 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.36 % Favored : 97.62 % Rotamer: Outliers : 2.34 % Allowed : 9.87 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % 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: 1.18 (0.12), residues: 4584 helix: 1.74 (0.10), residues: 2614 sheet: -0.31 (0.30), residues: 298 loop : -0.50 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M 47 HIS 0.008 0.001 HIS G 178 PHE 0.026 0.001 PHE L 341 TYR 0.021 0.001 TYR N 424 ARG 0.006 0.000 ARG G 664 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 461 time to evaluate : 4.736 Fit side-chains revert: symmetry clash REVERT: F 255 ARG cc_start: 0.8023 (mmt-90) cc_final: 0.7822 (mmt90) REVERT: F 330 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8578 (p0) REVERT: G 56 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8904 (mm-40) REVERT: G 405 GLU cc_start: 0.8752 (tt0) cc_final: 0.8522 (pt0) REVERT: G 617 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8501 (mp0) REVERT: C 36 ASP cc_start: 0.8754 (p0) cc_final: 0.8536 (p0) REVERT: C 597 ASP cc_start: 0.9008 (t0) cc_final: 0.8684 (t70) REVERT: I 147 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8504 (mp0) REVERT: I 153 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6521 (mmt) REVERT: H 152 GLN cc_start: 0.8589 (tt0) cc_final: 0.8369 (tt0) REVERT: H 228 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8424 (tt0) REVERT: H 273 LEU cc_start: 0.9084 (tp) cc_final: 0.8804 (mt) REVERT: H 298 MET cc_start: 0.8691 (mmp) cc_final: 0.8404 (mmp) REVERT: H 322 TRP cc_start: 0.8193 (t60) cc_final: 0.7790 (t-100) REVERT: A 36 PHE cc_start: 0.8404 (t80) cc_final: 0.8202 (t80) REVERT: L 77 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8496 (m-80) REVERT: L 105 TRP cc_start: 0.8196 (t60) cc_final: 0.7291 (m-10) REVERT: M 429 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7848 (tt) REVERT: M 447 LYS cc_start: 0.8743 (mmmt) cc_final: 0.8471 (mmtm) REVERT: N 1 MET cc_start: 0.6993 (mtp) cc_final: 0.5861 (ttp) REVERT: N 57 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8283 (mm110) REVERT: K 99 ARG cc_start: 0.8158 (ptp-170) cc_final: 0.7893 (ptp90) REVERT: J 64 MET cc_start: 0.9161 (mmp) cc_final: 0.8840 (mmp) REVERT: J 94 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8532 (mt) outliers start: 88 outliers final: 65 residues processed: 526 average time/residue: 0.5167 time to fit residues: 438.4194 Evaluate side-chains 523 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 450 time to evaluate : 4.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 721 ILE Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 521 SER Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 47 TRP Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 482 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 148 optimal weight: 0.3980 chunk 396 optimal weight: 5.9990 chunk 87 optimal weight: 0.0980 chunk 258 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 441 optimal weight: 10.0000 chunk 366 optimal weight: 9.9990 chunk 204 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 145 optimal weight: 9.9990 chunk 231 optimal weight: 0.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN F 425 GLN E 106 GLN E 119 GLN G 238 ASN G 901 HIS B 47 ASN ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN N 317 GLN N 404 GLN K 88 GLN J 24 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.245 37438 Z= 0.755 Angle : 2.188 50.653 50792 Z= 1.444 Chirality : 0.445 6.463 5683 Planarity : 0.004 0.066 6349 Dihedral : 8.647 167.778 5464 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.16 % Favored : 97.82 % Rotamer: Outliers : 2.39 % Allowed : 9.95 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % 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: 1.30 (0.12), residues: 4584 helix: 1.85 (0.10), residues: 2612 sheet: -0.25 (0.30), residues: 296 loop : -0.48 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP M 47 HIS 0.007 0.001 HIS G 178 PHE 0.026 0.001 PHE L 341 TYR 0.023 0.001 TYR N 424 ARG 0.007 0.000 ARG G 727 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 472 time to evaluate : 4.203 Fit side-chains REVERT: F 182 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8156 (tm-30) REVERT: E 91 TYR cc_start: 0.8321 (p90) cc_final: 0.8099 (p90) REVERT: G 405 GLU cc_start: 0.8755 (tt0) cc_final: 0.8555 (pt0) REVERT: G 617 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8467 (mp0) REVERT: G 901 HIS cc_start: 0.8435 (p90) cc_final: 0.8180 (p-80) REVERT: C 36 ASP cc_start: 0.8742 (p0) cc_final: 0.8528 (p0) REVERT: C 597 ASP cc_start: 0.8987 (t0) cc_final: 0.8744 (t0) REVERT: B 170 MET cc_start: 0.9030 (mmm) cc_final: 0.8814 (mmt) REVERT: B 174 GLU cc_start: 0.8694 (tt0) cc_final: 0.8423 (pt0) REVERT: I 147 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8311 (pp20) REVERT: I 153 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6489 (mmt) REVERT: H 152 GLN cc_start: 0.8560 (tt0) cc_final: 0.8353 (tt0) REVERT: H 273 LEU cc_start: 0.9069 (tp) cc_final: 0.8796 (mt) REVERT: H 298 MET cc_start: 0.8659 (mmp) cc_final: 0.8375 (mmp) REVERT: H 322 TRP cc_start: 0.8216 (t60) cc_final: 0.7796 (t-100) REVERT: L 77 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: L 105 TRP cc_start: 0.8185 (t60) cc_final: 0.7297 (m-10) REVERT: L 407 MET cc_start: 0.8607 (tpp) cc_final: 0.8096 (tpp) REVERT: M 429 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7760 (tt) REVERT: M 447 LYS cc_start: 0.8755 (mmmt) cc_final: 0.8513 (mmtm) REVERT: N 1 MET cc_start: 0.6945 (mtp) cc_final: 0.5753 (ttp) REVERT: N 57 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8453 (mm110) REVERT: K 88 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8446 (mp10) REVERT: K 99 ARG cc_start: 0.8154 (ptp-170) cc_final: 0.7890 (ptp90) REVERT: J 94 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8566 (mt) outliers start: 90 outliers final: 59 residues processed: 537 average time/residue: 0.5339 time to fit residues: 465.2747 Evaluate side-chains 523 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 457 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 721 ILE Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 47 TRP Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 482 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 425 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 251 optimal weight: 4.9990 chunk 322 optimal weight: 20.0000 chunk 249 optimal weight: 6.9990 chunk 371 optimal weight: 5.9990 chunk 246 optimal weight: 10.0000 chunk 439 optimal weight: 0.9990 chunk 275 optimal weight: 2.9990 chunk 267 optimal weight: 20.0000 chunk 202 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN E 106 GLN E 119 GLN G 238 ASN B 47 ASN ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN N 232 GLN ** N 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN J 24 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 37438 Z= 0.770 Angle : 2.195 50.659 50792 Z= 1.446 Chirality : 0.447 6.483 5683 Planarity : 0.004 0.068 6349 Dihedral : 8.687 167.782 5461 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.31 % Favored : 97.67 % Rotamer: Outliers : 2.39 % Allowed : 10.06 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % 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: 1.30 (0.12), residues: 4584 helix: 1.84 (0.10), residues: 2614 sheet: -0.25 (0.30), residues: 296 loop : -0.46 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M 47 HIS 0.007 0.001 HIS G 178 PHE 0.025 0.001 PHE L 341 TYR 0.020 0.001 TYR L 428 ARG 0.007 0.000 ARG G 664 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 460 time to evaluate : 4.271 Fit side-chains REVERT: F 182 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: G 405 GLU cc_start: 0.8745 (tt0) cc_final: 0.8538 (pt0) REVERT: G 617 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8512 (mp0) REVERT: C 36 ASP cc_start: 0.8746 (p0) cc_final: 0.8531 (p0) REVERT: C 389 LYS cc_start: 0.8930 (ttmm) cc_final: 0.8643 (tmtt) REVERT: I 147 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8509 (mp0) REVERT: I 153 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6507 (mmt) REVERT: H 152 GLN cc_start: 0.8597 (tt0) cc_final: 0.8381 (tt0) REVERT: H 273 LEU cc_start: 0.9078 (tp) cc_final: 0.8823 (mt) REVERT: H 284 LEU cc_start: 0.8567 (mm) cc_final: 0.8366 (mt) REVERT: H 298 MET cc_start: 0.8740 (mmp) cc_final: 0.8455 (mmp) REVERT: H 322 TRP cc_start: 0.8203 (t60) cc_final: 0.7778 (t-100) REVERT: L 77 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8497 (m-80) REVERT: L 105 TRP cc_start: 0.8183 (t60) cc_final: 0.7274 (m-10) REVERT: M 311 ILE cc_start: 0.8589 (pt) cc_final: 0.8236 (mt) REVERT: M 429 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7852 (tt) REVERT: N 1 MET cc_start: 0.6967 (mtp) cc_final: 0.5969 (ttp) REVERT: N 57 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8462 (mm110) REVERT: K 88 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8495 (mp10) REVERT: K 99 ARG cc_start: 0.8176 (ptp-170) cc_final: 0.7875 (ptp90) REVERT: J 64 MET cc_start: 0.9178 (mmp) cc_final: 0.8865 (mmp) REVERT: J 94 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8582 (mt) outliers start: 90 outliers final: 71 residues processed: 528 average time/residue: 0.5133 time to fit residues: 439.4896 Evaluate side-chains 534 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 456 time to evaluate : 4.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 656 SER Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 721 ILE Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 521 SER Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 47 TRP Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 482 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 271 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 262 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 279 optimal weight: 10.0000 chunk 299 optimal weight: 8.9990 chunk 217 optimal weight: 30.0000 chunk 40 optimal weight: 1.9990 chunk 345 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN E 106 GLN E 119 GLN G 238 ASN G 901 HIS B 47 ASN ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 232 GLN ** N 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN J 24 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 37438 Z= 0.777 Angle : 2.198 50.651 50792 Z= 1.448 Chirality : 0.448 6.463 5683 Planarity : 0.004 0.066 6349 Dihedral : 8.755 167.973 5461 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.29 % Favored : 97.69 % Rotamer: Outliers : 2.42 % Allowed : 10.16 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % 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: 1.26 (0.12), residues: 4584 helix: 1.79 (0.10), residues: 2623 sheet: -0.25 (0.30), residues: 296 loop : -0.46 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP M 47 HIS 0.007 0.001 HIS G 178 PHE 0.025 0.002 PHE L 341 TYR 0.021 0.002 TYR A 69 ARG 0.008 0.000 ARG G 664 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 454 time to evaluate : 4.682 Fit side-chains REVERT: F 182 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: G 405 GLU cc_start: 0.8762 (tt0) cc_final: 0.8549 (pt0) REVERT: G 617 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8531 (mp0) REVERT: C 36 ASP cc_start: 0.8751 (p0) cc_final: 0.8534 (p0) REVERT: C 389 LYS cc_start: 0.8940 (ttmm) cc_final: 0.8646 (tmtt) REVERT: C 469 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8876 (mp) REVERT: C 597 ASP cc_start: 0.8972 (t0) cc_final: 0.8568 (t70) REVERT: I 147 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8511 (mp0) REVERT: I 153 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.6508 (mmt) REVERT: H 59 GLN cc_start: 0.8845 (tm-30) cc_final: 0.7680 (mm-40) REVERT: H 152 GLN cc_start: 0.8595 (tt0) cc_final: 0.8379 (tt0) REVERT: H 273 LEU cc_start: 0.9108 (tp) cc_final: 0.8855 (mt) REVERT: H 298 MET cc_start: 0.8679 (mmp) cc_final: 0.8371 (mmp) REVERT: H 322 TRP cc_start: 0.8223 (t60) cc_final: 0.7801 (t-100) REVERT: L 77 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8496 (m-80) REVERT: L 105 TRP cc_start: 0.8170 (t60) cc_final: 0.7282 (m-10) REVERT: M 310 ASP cc_start: 0.8335 (t0) cc_final: 0.8047 (t0) REVERT: M 311 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8267 (mt) REVERT: M 429 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7859 (tt) REVERT: M 447 LYS cc_start: 0.8929 (mmmt) cc_final: 0.8421 (mtmt) REVERT: N 1 MET cc_start: 0.6795 (mtp) cc_final: 0.5893 (ttp) REVERT: N 57 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8456 (mm110) REVERT: K 88 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8483 (mp10) REVERT: K 99 ARG cc_start: 0.8191 (ptp-170) cc_final: 0.7887 (ptp90) REVERT: J 94 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8586 (mt) outliers start: 91 outliers final: 74 residues processed: 520 average time/residue: 0.5262 time to fit residues: 446.0876 Evaluate side-chains 532 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 449 time to evaluate : 4.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 261 HIS Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 656 SER Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 721 ILE Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 521 SER Chi-restraints excluded: chain M residue 47 TRP Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 482 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 399 optimal weight: 2.9990 chunk 421 optimal weight: 4.9990 chunk 384 optimal weight: 1.9990 chunk 409 optimal weight: 9.9990 chunk 420 optimal weight: 0.9990 chunk 246 optimal weight: 8.9990 chunk 178 optimal weight: 30.0000 chunk 321 optimal weight: 20.0000 chunk 125 optimal weight: 3.9990 chunk 370 optimal weight: 5.9990 chunk 387 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN E 106 GLN E 119 GLN G 238 ASN G 901 HIS B 43 ASN B 47 ASN ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN N 232 GLN ** N 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN J 24 ASN J 115 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 37438 Z= 0.764 Angle : 2.196 50.632 50792 Z= 1.447 Chirality : 0.447 6.429 5683 Planarity : 0.004 0.066 6349 Dihedral : 8.686 167.891 5461 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.23 % Favored : 97.75 % Rotamer: Outliers : 2.37 % Allowed : 10.35 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % 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: 1.30 (0.12), residues: 4584 helix: 1.82 (0.10), residues: 2626 sheet: -0.22 (0.30), residues: 296 loop : -0.45 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 135 HIS 0.007 0.001 HIS G 178 PHE 0.026 0.001 PHE H 268 TYR 0.020 0.001 TYR L 428 ARG 0.008 0.000 ARG G 664 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 455 time to evaluate : 4.584 Fit side-chains REVERT: F 182 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8184 (tm-30) REVERT: E 114 ASN cc_start: 0.8929 (t0) cc_final: 0.8676 (t0) REVERT: G 405 GLU cc_start: 0.8741 (tt0) cc_final: 0.8537 (pt0) REVERT: G 617 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8509 (mp0) REVERT: C 36 ASP cc_start: 0.8748 (p0) cc_final: 0.8532 (p0) REVERT: C 389 LYS cc_start: 0.8953 (ttmm) cc_final: 0.8662 (tmtt) REVERT: C 469 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8851 (mp) REVERT: C 597 ASP cc_start: 0.8981 (t0) cc_final: 0.8535 (t70) REVERT: I 147 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8515 (mp0) REVERT: I 153 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6487 (mmt) REVERT: H 152 GLN cc_start: 0.8585 (tt0) cc_final: 0.8366 (tt0) REVERT: H 273 LEU cc_start: 0.9080 (tp) cc_final: 0.8834 (mt) REVERT: H 298 MET cc_start: 0.8700 (mmp) cc_final: 0.8399 (mmp) REVERT: H 322 TRP cc_start: 0.8235 (t60) cc_final: 0.7884 (t-100) REVERT: L 77 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8463 (m-80) REVERT: L 105 TRP cc_start: 0.8139 (t60) cc_final: 0.7268 (m-10) REVERT: M 310 ASP cc_start: 0.8297 (t0) cc_final: 0.8005 (t0) REVERT: M 311 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8311 (mp) REVERT: M 429 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7834 (tt) REVERT: M 447 LYS cc_start: 0.8939 (mmmt) cc_final: 0.8433 (mtmt) REVERT: N 1 MET cc_start: 0.6811 (mtp) cc_final: 0.5908 (ttp) REVERT: N 57 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8456 (mm110) REVERT: K 88 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8498 (mp10) REVERT: K 99 ARG cc_start: 0.8173 (ptp-170) cc_final: 0.7862 (ptp90) REVERT: J 94 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8587 (mt) outliers start: 89 outliers final: 71 residues processed: 518 average time/residue: 0.5236 time to fit residues: 439.4657 Evaluate side-chains 531 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 451 time to evaluate : 4.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 261 HIS Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 656 SER Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 721 ILE Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 521 SER Chi-restraints excluded: chain M residue 47 TRP Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 482 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 408 optimal weight: 9.9990 chunk 268 optimal weight: 10.0000 chunk 433 optimal weight: 0.8980 chunk 264 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 301 optimal weight: 9.9990 chunk 454 optimal weight: 9.9990 chunk 418 optimal weight: 8.9990 chunk 361 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 279 optimal weight: 5.9990 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN E 106 GLN G 238 ASN G 901 HIS B 47 ASN ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN N 232 GLN ** N 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 37438 Z= 0.767 Angle : 2.196 50.632 50792 Z= 1.447 Chirality : 0.447 6.439 5683 Planarity : 0.004 0.067 6349 Dihedral : 8.662 167.787 5461 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.36 % Favored : 97.62 % Rotamer: Outliers : 2.39 % Allowed : 10.40 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % 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: 1.31 (0.12), residues: 4584 helix: 1.84 (0.10), residues: 2612 sheet: -0.23 (0.30), residues: 296 loop : -0.43 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 135 HIS 0.007 0.001 HIS G 178 PHE 0.026 0.001 PHE L 341 TYR 0.021 0.001 TYR L 428 ARG 0.009 0.000 ARG G 664 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 453 time to evaluate : 4.173 Fit side-chains REVERT: F 182 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8130 (tm-30) REVERT: E 114 ASN cc_start: 0.8980 (t0) cc_final: 0.8729 (t0) REVERT: G 617 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8513 (mp0) REVERT: C 36 ASP cc_start: 0.8747 (p0) cc_final: 0.8531 (p0) REVERT: C 389 LYS cc_start: 0.8962 (ttmm) cc_final: 0.8667 (tmtt) REVERT: C 469 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8854 (mp) REVERT: C 597 ASP cc_start: 0.8973 (t0) cc_final: 0.8528 (t70) REVERT: I 147 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8517 (mp0) REVERT: I 153 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6493 (mmt) REVERT: H 59 GLN cc_start: 0.8844 (tm-30) cc_final: 0.7659 (mm-40) REVERT: H 152 GLN cc_start: 0.8629 (tt0) cc_final: 0.8415 (tt0) REVERT: H 298 MET cc_start: 0.8748 (mmp) cc_final: 0.8456 (mmp) REVERT: H 322 TRP cc_start: 0.8234 (t60) cc_final: 0.7883 (t-100) REVERT: A 30 MET cc_start: 0.8012 (tpp) cc_final: 0.7793 (ttm) REVERT: L 77 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8480 (m-80) REVERT: L 105 TRP cc_start: 0.8130 (t60) cc_final: 0.7236 (m-10) REVERT: M 310 ASP cc_start: 0.8306 (t0) cc_final: 0.8009 (t0) REVERT: M 311 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8319 (mp) REVERT: M 429 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7835 (tt) REVERT: M 447 LYS cc_start: 0.8947 (mmmt) cc_final: 0.8444 (mtmt) REVERT: N 1 MET cc_start: 0.6894 (mtp) cc_final: 0.6033 (ttp) REVERT: N 57 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8455 (mm110) REVERT: K 88 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8509 (mp10) REVERT: K 99 ARG cc_start: 0.8193 (ptp-170) cc_final: 0.7882 (ptp90) REVERT: J 94 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8569 (mt) outliers start: 90 outliers final: 73 residues processed: 516 average time/residue: 0.5246 time to fit residues: 441.8653 Evaluate side-chains 530 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 448 time to evaluate : 4.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 656 SER Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 721 ILE Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 792 GLU Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 521 SER Chi-restraints excluded: chain M residue 47 TRP Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 482 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 221 optimal weight: 5.9990 chunk 287 optimal weight: 4.9990 chunk 385 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 333 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 362 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 372 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN F 425 GLN E 106 GLN G 238 ASN G 901 HIS B 47 ASN ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 232 GLN ** N 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.079944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.060189 restraints weight = 59302.260| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 1.42 r_work: 0.2652 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.245 37438 Z= 0.757 Angle : 2.192 50.621 50792 Z= 1.445 Chirality : 0.445 6.392 5683 Planarity : 0.004 0.066 6349 Dihedral : 8.537 167.557 5461 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.16 % Favored : 97.82 % Rotamer: Outliers : 2.15 % Allowed : 10.83 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % 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: 1.39 (0.12), residues: 4584 helix: 1.89 (0.10), residues: 2614 sheet: -0.18 (0.30), residues: 296 loop : -0.39 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP M 47 HIS 0.007 0.001 HIS G 178 PHE 0.026 0.001 PHE L 341 TYR 0.022 0.001 TYR N 424 ARG 0.008 0.000 ARG G 664 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9694.78 seconds wall clock time: 175 minutes 25.35 seconds (10525.35 seconds total)