Starting phenix.real_space_refine on Fri Feb 23 03:30:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p62_13215/02_2024/7p62_13215_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p62_13215/02_2024/7p62_13215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p62_13215/02_2024/7p62_13215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p62_13215/02_2024/7p62_13215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p62_13215/02_2024/7p62_13215_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p62_13215/02_2024/7p62_13215_updated.pdb" } resolution = 3.6 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= 0.009 sd= 0.034 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 3 5.49 5 S 266 5.16 5 C 23760 2.51 5 N 6090 2.21 5 O 6445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 275": "OE1" <-> "OE2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "G GLU 337": "OE1" <-> "OE2" Residue "G GLU 382": "OE1" <-> "OE2" Residue "G GLU 792": "OE1" <-> "OE2" Residue "C PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 453": "OE1" <-> "OE2" Residue "B TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "I GLU 147": "OE1" <-> "OE2" Residue "L GLU 111": "OE1" <-> "OE2" Residue "L TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 202": "OE1" <-> "OE2" Residue "L GLU 401": "OE1" <-> "OE2" Residue "N GLU 200": "OE1" <-> "OE2" Residue "N GLU 267": "OE1" <-> "OE2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H GLU 36": "OE1" <-> "OE2" Residue "H GLU 216": "OE1" <-> "OE2" Residue "H PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 241": "OE1" <-> "OE2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "J GLU 82": "OE1" <-> "OE2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36597 Number of models: 1 Model: "" Number of chains: 19 Chain: "F" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3432 Classifications: {'peptide': 442} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 416} 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: {'PTRANS': 9, '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: 4644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4644 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 538} Chain breaks: 2 Chain: "B" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1529 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 178} Chain breaks: 3 Chain: "I" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1140 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "L" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4530 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 576} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 482} Chain: "N" Number of atoms: 3638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3638 Classifications: {'peptide': 480} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 459} Chain breaks: 1 Chain: "H" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2422 Classifications: {'peptide': 308} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Chain: "A" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 797 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} 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: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1312 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 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: "L" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2746 SG CYS F 354 70.227 61.343 195.693 1.00 72.41 S ATOM 2766 SG CYS F 357 73.713 61.382 200.392 1.00 62.06 S ATOM 3087 SG CYS F 398 68.003 57.984 200.878 1.00 61.07 S ATOM 2722 SG CYS F 351 72.530 55.298 197.490 1.00 38.66 S ATOM 4079 SG CYS E 92 81.233 53.588 217.380 1.00 95.27 S ATOM 4113 SG CYS E 97 81.128 54.463 220.799 1.00 86.52 S ATOM 4391 SG CYS E 133 76.459 52.654 216.479 1.00 79.11 S ATOM 4417 SG CYS E 137 75.156 53.566 219.927 1.00 88.78 S ATOM 5501 SG CYS G 114 80.931 66.816 178.092 1.00 44.59 S ATOM 5441 SG CYS G 105 86.259 70.401 179.944 1.00 73.92 S ATOM 5461 SG CYS G 108 86.824 64.512 177.379 1.00 31.55 S ATOM 5855 SG CYS G 156 74.889 59.329 183.411 1.00 68.70 S ATOM 5836 SG CYS G 153 80.736 58.504 186.377 1.00 39.33 S ATOM 5884 SG CYS G 159 77.999 53.620 183.010 1.00 35.66 S ATOM 6228 SG CYS G 203 80.100 58.669 179.772 1.00 63.71 S ATOM 6453 SG CYS G 230 76.891 49.222 158.850 1.00 60.79 S ATOM 6738 SG CYS G 265 76.791 45.831 164.474 1.00 55.13 S ATOM 6501 SG CYS G 237 71.523 48.998 162.048 1.00 58.15 S ATOM 6477 SG CYS G 233 73.882 43.462 159.243 1.00 94.24 S ATOM 4902 SG CYS G 36 68.608 60.415 186.012 1.00 38.38 S ATOM 4978 SG CYS G 47 70.019 63.642 186.524 1.00 35.57 S ATOM 5004 SG CYS G 50 64.188 65.304 186.143 1.00 92.28 S ATOM 5153 SG CYS G 69 63.924 61.453 185.902 1.00 65.53 S ATOM 17125 SG CYS B 129 92.011 93.349 153.530 1.00 72.15 S ATOM 16737 SG CYS B 64 96.931 97.814 154.754 1.00113.88 S ATOM 16731 SG CYS B 63 90.796 99.099 156.084 1.00119.36 S ATOM 17342 SG CYS B 158 93.552 94.320 159.440 1.00 92.82 S ATOM 18377 SG CYS I 102 91.615 87.711 165.481 1.00 50.55 S ATOM 18352 SG CYS I 99 96.930 86.174 161.741 1.00 60.38 S ATOM 18395 SG CYS I 105 95.766 83.096 167.308 1.00 35.38 S ATOM 18110 SG CYS I 70 91.754 82.304 162.115 1.00 58.64 S ATOM 18424 SG CYS I 109 96.748 77.717 173.976 1.00 36.79 S ATOM 18087 SG CYS I 66 94.794 76.864 167.847 1.00 48.87 S ATOM 18047 SG CYS I 60 99.132 72.687 170.419 1.00 28.65 S ATOM 18065 SG CYS I 63 92.787 72.970 172.480 1.00 21.83 S Time building chain proxies: 19.42, per 1000 atoms: 0.53 Number of scatterers: 36597 At special positions: 0 Unit cell: (158.089, 215.383, 250.396, 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 266 16.00 P 3 15.00 O 6445 8.00 N 6090 7.00 C 23760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.22 Conformation dependent library (CDL) restraints added in 7.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb=" SF4 B 301 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " 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="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb=" SF4 G1003 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " 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="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8544 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 186 helices and 25 sheets defined 52.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.34 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 removed outlier: 3.659A pdb=" N LEU F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 138 through 152 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 234 through 237 No H-bonds generated for 'chain 'F' and resid 234 through 237' Processing helix chain 'F' and resid 270 through 275 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 312 through 315 No H-bonds generated for 'chain 'F' and resid 312 through 315' 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 381 through 390 Processing helix chain 'F' and resid 400 through 413 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: 3.671A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.654A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG E 47 " --> pdb=" O GLN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.065A 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 100 Processing helix chain 'E' and resid 103 through 112 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 155 through 164 removed outlier: 3.652A pdb=" N ILE E 158 " --> pdb=" O PRO E 155 " (cutoff:3.500A) Proline residue: E 159 - end of helix removed outlier: 3.525A pdb=" N LEU E 162 " --> pdb=" O PRO E 159 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU E 163 " --> pdb=" O GLU E 160 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG E 164 " --> pdb=" O LEU E 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 155 through 164' Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 97 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'G' and resid 115 through 123 Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 196 through 202 removed outlier: 3.670A pdb=" N VAL G 200 " --> pdb=" O GLY G 197 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE G 202 " --> pdb=" O LEU G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 214 No H-bonds generated for 'chain 'G' and resid 211 through 214' Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 333 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 389 through 410 removed outlier: 4.174A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN G 410 " --> pdb=" O MET G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 424 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 504 through 506 No H-bonds generated for 'chain 'G' and resid 504 through 506' 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 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 685 No H-bonds generated for 'chain 'G' and resid 683 through 685' Processing helix chain 'G' and resid 699 through 701 No H-bonds generated for 'chain 'G' and resid 699 through 701' Processing helix chain 'G' and resid 764 through 770 removed outlier: 3.702A pdb=" N TRP G 767 " --> pdb=" O PRO G 764 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN G 768 " --> pdb=" O GLN G 765 " (cutoff:3.500A) Processing helix chain 'G' and resid 825 through 828 No H-bonds generated for 'chain 'G' and resid 825 through 828' 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 65 Processing helix chain 'C' and resid 132 through 144 removed outlier: 3.898A pdb=" N ASN C 135 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TRP C 136 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (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 281 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 327 Processing helix chain 'C' and resid 337 through 353 removed outlier: 3.948A pdb=" N THR C 341 " --> pdb=" O PHE C 337 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASP C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 384 Processing helix chain 'C' and resid 388 through 400 Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 418 through 421 No H-bonds generated for 'chain 'C' and resid 418 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 removed outlier: 3.999A pdb=" N VAL C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) 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 598 No H-bonds generated for 'chain 'C' and resid 595 through 598' Processing helix chain 'B' and resid 37 through 52 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 127 through 131 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 177 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 107 No H-bonds generated for 'chain 'I' and resid 104 through 107' Processing helix chain 'I' and resid 128 through 130 No H-bonds generated for 'chain 'I' and resid 128 through 130' Processing helix chain 'L' and resid 4 through 19 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 27 through 55 removed outlier: 4.345A pdb=" N VAL L 38 " --> pdb=" O GLY L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 131 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 191 Processing helix chain 'L' and resid 197 through 207 removed outlier: 3.630A pdb=" N GLU L 202 " --> pdb=" O ARG L 198 " (cutoff:3.500A) Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 216 through 230 Processing helix chain 'L' and resid 233 through 235 No H-bonds generated for 'chain 'L' and resid 233 through 235' Processing helix chain 'L' and resid 241 through 243 No H-bonds generated for 'chain 'L' and resid 241 through 243' Processing helix chain 'L' and resid 247 through 255 Processing helix chain 'L' and resid 261 through 268 Processing helix chain 'L' and resid 270 through 273 No H-bonds generated for 'chain 'L' and resid 270 through 273' Processing helix chain 'L' and resid 277 through 298 Processing helix chain 'L' and resid 304 through 325 Processing helix chain 'L' and resid 328 through 355 Processing helix chain 'L' and resid 368 through 370 No H-bonds generated for 'chain 'L' and resid 368 through 370' Processing helix chain 'L' and resid 373 through 387 Processing helix chain 'L' and resid 394 through 409 removed outlier: 4.028A pdb=" N ASN L 409 " --> pdb=" O GLY L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 413 through 434 Processing helix chain 'L' and resid 455 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 490 through 512 Processing helix chain 'L' and resid 517 through 523 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 538 through 549 removed outlier: 6.051A pdb=" N ASP L 542 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP L 543 " --> pdb=" O GLY L 540 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU L 544 " --> pdb=" O PHE L 541 " (cutoff:3.500A) Processing helix chain 'L' and resid 551 through 559 Processing helix chain 'L' and resid 564 through 586 Proline residue: L 572 - end of helix removed outlier: 3.841A pdb=" N LEU L 585 " --> pdb=" O LYS L 581 " (cutoff:3.500A) removed outlier: 4.566A 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 21 Proline residue: M 10 - end of helix removed outlier: 4.155A pdb=" N GLU M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 49 Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 114 through 132 Processing helix chain 'M' and resid 136 through 143 Processing helix chain 'M' and resid 145 through 157 Proline residue: M 149 - end of helix Processing helix chain 'M' and resid 164 through 199 Processing helix chain 'M' and resid 219 through 234 removed outlier: 4.062A pdb=" N LYS M 234 " --> pdb=" O ALA M 230 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 249 removed outlier: 4.081A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 261 Processing helix chain 'M' and resid 267 through 274 Processing helix chain 'M' and resid 280 through 307 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 377 through 379 No H-bonds generated for 'chain 'M' and resid 377 through 379' Processing helix chain 'M' and resid 384 through 396 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 444 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 501 removed outlier: 4.823A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ALA M 492 " --> pdb=" O THR M 488 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 8 Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 35 through 57 Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.146A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 120 Processing helix chain 'N' and resid 125 through 146 Proline residue: N 138 - end of helix removed outlier: 4.049A pdb=" N GLY N 141 " --> pdb=" O LEU N 137 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA N 146 " --> pdb=" O LEU N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 180 Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.960A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 removed outlier: 3.805A pdb=" N ASP N 265 " --> pdb=" O PRO N 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 262 through 265' Processing helix chain 'N' and resid 269 through 287 Processing helix chain 'N' and resid 294 through 319 removed outlier: 4.076A pdb=" N ALA N 315 " --> pdb=" O VAL N 311 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU N 316 " --> pdb=" O ALA N 312 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLN N 317 " --> pdb=" O LEU N 313 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N THR N 318 " --> pdb=" O ILE N 314 " (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 384 removed outlier: 3.727A pdb=" N ALA N 384 " --> pdb=" O MET N 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.117A pdb=" N TYR N 423 " --> pdb=" O ALA N 419 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR N 424 " --> pdb=" O ILE N 420 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 480 Processing helix chain 'H' and resid 6 through 39 removed outlier: 3.797A pdb=" N PHE H 34 " --> pdb=" O ALA H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 removed outlier: 3.639A pdb=" N LEU H 60 " --> pdb=" O SER H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 100 Proline residue: H 87 - end of helix removed outlier: 4.717A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE H 98 " --> pdb=" O LEU H 94 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 136 removed outlier: 4.271A pdb=" N VAL H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 5.128A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.303A 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 210 through 212 No H-bonds generated for 'chain 'H' and resid 210 through 212' Processing helix chain 'H' and resid 215 through 218 removed outlier: 4.334A pdb=" N GLU H 218 " --> pdb=" O PRO H 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 215 through 218' Processing helix chain 'H' and resid 232 through 256 removed outlier: 3.946A pdb=" N PHE H 237 " --> pdb=" O LYS H 233 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TYR H 242 " --> pdb=" O PHE H 238 " (cutoff:3.500A) 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 322 Processing helix chain 'A' and resid 9 through 36 Processing helix chain 'A' and resid 67 through 91 removed outlier: 3.557A pdb=" N TYR A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 120 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 53 removed outlier: 3.574A pdb=" N TRP K 53 " --> pdb=" O ALA K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 87 Processing helix chain 'J' and resid 3 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 90 through 111 removed outlier: 4.970A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 126 through 131 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: 6.761A pdb=" N TYR F 86 " --> pdb=" O CYS F 215 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ASN F 217 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU F 88 " --> pdb=" O ASN F 217 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU F 87 " --> pdb=" O TYR F 126 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY F 128 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N CYS F 89 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE F 130 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N HIS F 172 " --> pdb=" O LEU F 132 " (cutoff:3.500A) 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 289 through 291 Processing sheet with id= D, first strand: chain 'E' and resid 127 through 131 Processing sheet with id= E, first strand: chain 'G' and resid 5 through 8 Processing sheet with id= F, first strand: chain 'G' and resid 64 through 67 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: 6.349A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.433A 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: 6.937A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU G 591 " --> pdb=" O VAL G 566 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL G 568 " --> pdb=" O LEU G 591 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N MET G 593 " --> pdb=" O VAL G 568 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU G 610 " --> pdb=" O ASP G 596 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'G' and resid 530 through 534 removed outlier: 6.358A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL G 379 " --> pdb=" O PRO G 430 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE G 432 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.629A 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 901 through 903 Processing sheet with id= O, first strand: chain 'G' and resid 841 through 844 removed outlier: 7.827A pdb=" N ILE G 842 " --> pdb=" O THR G 870 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU G 844 " --> pdb=" O PRO G 872 " (cutoff:3.500A) removed outlier: 5.897A 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: 4.294A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.389A 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: 6.393A 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 220 removed outlier: 3.911A pdb=" N ARG C 232 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP C 244 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 532 through 538 Processing sheet with id= T, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.630A pdb=" N VAL B 192 " --> pdb=" O THR B 6 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.951A pdb=" N LEU B 95 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'I' and resid 75 through 81 removed outlier: 3.626A pdb=" N GLN I 78 " --> pdb=" O PHE I 91 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 60 through 63 Processing sheet with id= X, first strand: chain 'L' and resid 66 through 70 removed outlier: 6.918A pdb=" N ILE L 75 " --> pdb=" O TRP L 67 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER L 69 " --> pdb=" O PHE L 73 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE L 73 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.851A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) 1744 hydrogen bonds defined for protein. 5055 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: 12.56 Time building geometry restraints manager: 16.51 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: 15684 1.42 - 1.64: 21336 1.64 - 1.87: 407 1.87 - 2.09: 0 2.09 - 2.31: 92 Bond restraints: 37519 Sorted by residual: bond pdb=" C THR F 355 " pdb=" N PRO F 356 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.30e-02 5.92e+03 1.32e+01 bond pdb=" C ILE H 190 " pdb=" N PRO H 191 " ideal model delta sigma weight residual 1.336 1.378 -0.042 1.23e-02 6.61e+03 1.18e+01 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 8.72e+00 bond pdb=" O13 3PE L 802 " pdb=" P 3PE L 802 " ideal model delta sigma weight residual 1.654 1.597 0.057 2.00e-02 2.50e+03 8.22e+00 bond pdb=" O11 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.644 1.595 0.049 2.00e-02 2.50e+03 5.98e+00 ... (remaining 37514 not shown) Histogram of bond angle deviations from ideal: 70.13 - 83.01: 88 83.01 - 95.89: 1 95.89 - 108.77: 2283 108.77 - 121.65: 40468 121.65 - 134.53: 8149 Bond angle restraints: 50989 Sorted by residual: angle pdb=" CA PRO G 840 " pdb=" N PRO G 840 " pdb=" CD PRO G 840 " ideal model delta sigma weight residual 112.00 104.17 7.83 1.40e+00 5.10e-01 3.13e+01 angle pdb=" CA PRO M 61 " pdb=" N PRO M 61 " pdb=" CD PRO M 61 " ideal model delta sigma weight residual 112.00 104.29 7.71 1.40e+00 5.10e-01 3.03e+01 angle pdb=" C PRO N 387 " pdb=" N MET N 388 " pdb=" CA MET N 388 " ideal model delta sigma weight residual 122.61 130.42 -7.81 1.56e+00 4.11e-01 2.51e+01 angle pdb=" C LEU M 264 " pdb=" CA LEU M 264 " pdb=" CB LEU M 264 " ideal model delta sigma weight residual 117.23 110.43 6.80 1.36e+00 5.41e-01 2.50e+01 angle pdb=" N MET C 387 " pdb=" CA MET C 387 " pdb=" C MET C 387 " ideal model delta sigma weight residual 109.81 120.29 -10.48 2.21e+00 2.05e-01 2.25e+01 ... (remaining 50984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.90: 21337 33.90 - 67.79: 592 67.79 - 101.69: 36 101.69 - 135.59: 0 135.59 - 169.48: 1 Dihedral angle restraints: 21966 sinusoidal: 8613 harmonic: 13353 Sorted by residual: dihedral pdb=" CA CYS B 158 " pdb=" C CYS B 158 " pdb=" N PRO B 159 " pdb=" CA PRO B 159 " ideal model delta harmonic sigma weight residual -180.00 -120.35 -59.65 0 5.00e+00 4.00e-02 1.42e+02 dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 88.11 169.48 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" CA PRO F 201 " pdb=" C PRO F 201 " pdb=" N PRO F 202 " pdb=" CA PRO F 202 " ideal model delta harmonic sigma weight residual 180.00 149.38 30.62 0 5.00e+00 4.00e-02 3.75e+01 ... (remaining 21963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.238: 5711 4.238 - 8.476: 0 8.476 - 12.714: 0 12.714 - 16.951: 0 16.951 - 21.189: 28 Chirality restraints: 5739 Sorted by residual: chirality pdb="FE3 SF4 G1001 " pdb=" S1 SF4 G1001 " pdb=" S2 SF4 G1001 " pdb=" S4 SF4 G1001 " both_signs ideal model delta sigma weight residual False -10.55 10.63 -21.19 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 -10.62 21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 B 301 " pdb=" S1 SF4 B 301 " pdb=" S2 SF4 B 301 " pdb=" S3 SF4 B 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.62 21.17 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5736 not shown) Planarity restraints: 6410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE M 60 " -0.108 5.00e-02 4.00e+02 1.62e-01 4.18e+01 pdb=" N PRO M 61 " 0.280 5.00e-02 4.00e+02 pdb=" CA PRO M 61 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO M 61 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN G 839 " -0.085 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO G 840 " 0.216 5.00e-02 4.00e+02 pdb=" CA PRO G 840 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO G 840 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR N 4 " -0.065 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO N 5 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO N 5 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO N 5 " -0.053 5.00e-02 4.00e+02 ... (remaining 6407 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3991 2.75 - 3.29: 36056 3.29 - 3.83: 65745 3.83 - 4.36: 76434 4.36 - 4.90: 131929 Nonbonded interactions: 314155 Sorted by model distance: nonbonded pdb=" OG SER G 739 " pdb=" OE1 GLU G 741 " model vdw 2.217 2.440 nonbonded pdb=" O TYR N 159 " pdb=" OG SER N 163 " model vdw 2.232 2.440 nonbonded pdb=" OD1 ASP L 563 " pdb=" OH TYR M 300 " model vdw 2.244 2.440 nonbonded pdb=" OH TYR G 255 " pdb=" O GLY G 776 " model vdw 2.250 2.440 nonbonded pdb=" O ALA M 316 " pdb=" OG SER M 319 " model vdw 2.254 2.440 ... (remaining 314150 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 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: 0.030 Extract box with map and model: 3.920 Check model and map are aligned: 0.510 Set scattering table: 0.260 Process input model: 103.260 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 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 : 0.004 0.113 37519 Z= 0.250 Angle : 0.826 13.381 50989 Z= 0.421 Chirality : 1.477 21.189 5739 Planarity : 0.007 0.162 6410 Dihedral : 15.119 169.485 13422 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.45 % Allowed : 16.58 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.11), residues: 4629 helix: -0.19 (0.10), residues: 2561 sheet: -0.99 (0.29), residues: 288 loop : -1.66 (0.13), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 386 HIS 0.008 0.001 HIS G 429 PHE 0.034 0.002 PHE H 277 TYR 0.040 0.002 TYR M 435 ARG 0.015 0.000 ARG J 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 527 time to evaluate : 4.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 82 MET cc_start: 0.8302 (mtp) cc_final: 0.8002 (mtt) REVERT: E 144 MET cc_start: 0.9198 (mtm) cc_final: 0.8873 (mtp) REVERT: G 310 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8512 (mm-40) REVERT: G 728 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7720 (pt0) REVERT: G 855 ASN cc_start: 0.8465 (t0) cc_final: 0.7971 (p0) REVERT: C 62 ASP cc_start: 0.8772 (t0) cc_final: 0.8363 (t0) REVERT: C 273 ASP cc_start: 0.8436 (m-30) cc_final: 0.8138 (m-30) REVERT: B 27 ASP cc_start: 0.8160 (p0) cc_final: 0.7620 (p0) REVERT: B 135 MET cc_start: 0.8518 (ptm) cc_final: 0.8306 (ttp) REVERT: B 178 LYS cc_start: 0.8933 (mtmm) cc_final: 0.8646 (mtpp) REVERT: I 119 ASP cc_start: 0.8445 (t0) cc_final: 0.8238 (t0) REVERT: I 124 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8637 (mm-30) REVERT: L 43 LEU cc_start: 0.8537 (mm) cc_final: 0.8301 (tt) REVERT: L 319 MET cc_start: 0.8249 (mmt) cc_final: 0.7987 (mmt) REVERT: L 476 GLN cc_start: 0.8543 (mp10) cc_final: 0.7959 (pm20) REVERT: M 223 LEU cc_start: 0.9118 (mt) cc_final: 0.8887 (mt) REVERT: M 439 MET cc_start: 0.9054 (tmm) cc_final: 0.8805 (tmm) REVERT: N 61 MET cc_start: 0.8172 (ptm) cc_final: 0.7839 (pmm) REVERT: N 306 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8605 (mm) REVERT: H 165 MET cc_start: 0.7932 (mmt) cc_final: 0.7695 (mmp) REVERT: H 229 TYR cc_start: 0.9271 (m-80) cc_final: 0.8778 (m-10) REVERT: H 241 GLU cc_start: 0.7594 (mt-10) cc_final: 0.6933 (tm-30) REVERT: A 85 LEU cc_start: 0.8530 (mt) cc_final: 0.7417 (mp) REVERT: A 94 GLU cc_start: 0.9400 (mp0) cc_final: 0.9120 (mp0) REVERT: J 44 PHE cc_start: 0.8987 (m-80) cc_final: 0.8629 (m-10) REVERT: J 73 MET cc_start: 0.8847 (ttm) cc_final: 0.8557 (ttm) REVERT: J 86 GLN cc_start: 0.8678 (mm110) cc_final: 0.8461 (mm110) REVERT: J 87 TRP cc_start: 0.8502 (p90) cc_final: 0.8242 (p90) REVERT: J 89 LYS cc_start: 0.7636 (mmtm) cc_final: 0.7149 (mmtt) outliers start: 17 outliers final: 8 residues processed: 538 average time/residue: 0.4749 time to fit residues: 419.6126 Evaluate side-chains 492 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 483 time to evaluate : 3.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain L residue 512 TRP Chi-restraints excluded: chain N residue 306 LEU Chi-restraints excluded: chain J residue 74 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 390 optimal weight: 4.9990 chunk 350 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 236 optimal weight: 7.9990 chunk 187 optimal weight: 20.0000 chunk 362 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 220 optimal weight: 2.9990 chunk 270 optimal weight: 10.0000 chunk 420 optimal weight: 8.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 341 ASN F 400 HIS ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 HIS ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 GLN G 867 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 HIS ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN I 64 ASN L 163 ASN L 438 HIS H 214 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.266 37519 Z= 0.778 Angle : 2.218 51.614 50989 Z= 1.455 Chirality : 0.439 6.645 5739 Planarity : 0.005 0.109 6410 Dihedral : 6.434 167.997 5166 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.88 % Allowed : 15.63 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.12), residues: 4629 helix: 0.60 (0.10), residues: 2588 sheet: -0.87 (0.29), residues: 315 loop : -1.45 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 73 HIS 0.006 0.001 HIS M 348 PHE 0.025 0.002 PHE L 430 TYR 0.022 0.001 TYR L 428 ARG 0.007 0.000 ARG G 804 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 488 time to evaluate : 4.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 316 LYS cc_start: 0.8779 (mtmm) cc_final: 0.8331 (mmtt) REVERT: G 308 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8804 (mp) REVERT: G 728 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7866 (pt0) REVERT: G 855 ASN cc_start: 0.8586 (t0) cc_final: 0.8377 (t0) REVERT: C 273 ASP cc_start: 0.8682 (m-30) cc_final: 0.8457 (m-30) REVERT: C 381 ARG cc_start: 0.8587 (tpp80) cc_final: 0.8287 (tpp-160) REVERT: B 27 ASP cc_start: 0.8453 (p0) cc_final: 0.7932 (p0) REVERT: B 59 PHE cc_start: 0.7707 (t80) cc_final: 0.7461 (t80) REVERT: B 174 GLU cc_start: 0.8643 (pt0) cc_final: 0.8399 (pt0) REVERT: B 178 LYS cc_start: 0.9109 (mtmm) cc_final: 0.8848 (mmtt) REVERT: L 200 MET cc_start: 0.8144 (mtm) cc_final: 0.7887 (mtm) REVERT: L 216 MET cc_start: 0.8369 (mtt) cc_final: 0.8017 (mtt) REVERT: L 319 MET cc_start: 0.8512 (mmt) cc_final: 0.8271 (mmt) REVERT: L 424 MET cc_start: 0.8071 (ppp) cc_final: 0.7678 (ppp) REVERT: L 476 GLN cc_start: 0.8593 (mp10) cc_final: 0.8018 (pm20) REVERT: M 153 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8726 (mp) REVERT: M 323 MET cc_start: 0.8089 (mmm) cc_final: 0.7753 (mmm) REVERT: M 398 MET cc_start: 0.8054 (tpp) cc_final: 0.7168 (tpp) REVERT: N 20 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8689 (p) REVERT: N 61 MET cc_start: 0.8273 (ptm) cc_final: 0.7919 (pmm) REVERT: N 321 MET cc_start: 0.8618 (ptp) cc_final: 0.8378 (ptm) REVERT: H 214 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7221 (pp30) REVERT: H 293 ARG cc_start: 0.8661 (mtm110) cc_final: 0.8324 (mtm-85) REVERT: A 85 LEU cc_start: 0.8450 (mt) cc_final: 0.8018 (mt) REVERT: J 142 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7926 (mm-30) outliers start: 110 outliers final: 69 residues processed: 566 average time/residue: 0.4997 time to fit residues: 463.5124 Evaluate side-chains 538 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 465 time to evaluate : 3.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 647 MET Chi-restraints excluded: chain G residue 867 ASN Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 512 TRP Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 306 LEU Chi-restraints excluded: chain N residue 403 VAL Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 214 GLN Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 120 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 233 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 349 optimal weight: 8.9990 chunk 286 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 421 optimal weight: 5.9990 chunk 455 optimal weight: 9.9990 chunk 375 optimal weight: 2.9990 chunk 417 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 337 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 110 HIS F 196 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN I 168 ASN L 121 ASN N 7 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.249 37519 Z= 0.780 Angle : 2.215 50.687 50989 Z= 1.453 Chirality : 0.444 6.523 5739 Planarity : 0.005 0.099 6410 Dihedral : 6.386 166.269 5156 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.40 % Allowed : 16.50 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.12), residues: 4629 helix: 0.85 (0.10), residues: 2596 sheet: -0.71 (0.29), residues: 306 loop : -1.37 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP H 135 HIS 0.006 0.001 HIS G 101 PHE 0.026 0.002 PHE L 430 TYR 0.020 0.002 TYR L 428 ARG 0.010 0.001 ARG G 804 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 477 time to evaluate : 4.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 37 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8547 (mt) REVERT: E 78 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: E 93 ASP cc_start: 0.8382 (t0) cc_final: 0.8066 (t0) REVERT: G 308 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8755 (mp) REVERT: G 517 ASN cc_start: 0.8710 (m-40) cc_final: 0.8499 (m110) REVERT: G 855 ASN cc_start: 0.8633 (t0) cc_final: 0.8408 (t0) REVERT: C 62 ASP cc_start: 0.9147 (t0) cc_final: 0.8780 (t0) REVERT: C 273 ASP cc_start: 0.8733 (m-30) cc_final: 0.8442 (m-30) REVERT: C 381 ARG cc_start: 0.8632 (tpp80) cc_final: 0.8372 (tpp-160) REVERT: B 174 GLU cc_start: 0.8744 (pt0) cc_final: 0.8470 (pt0) REVERT: B 178 LYS cc_start: 0.9153 (mtmm) cc_final: 0.8873 (mmtt) REVERT: I 84 ASP cc_start: 0.8922 (p0) cc_final: 0.8605 (p0) REVERT: L 216 MET cc_start: 0.8305 (mtt) cc_final: 0.7971 (mtt) REVERT: L 319 MET cc_start: 0.8622 (mmt) cc_final: 0.8325 (mmt) REVERT: L 424 MET cc_start: 0.8018 (ppp) cc_final: 0.7462 (ppp) REVERT: L 476 GLN cc_start: 0.8595 (mp10) cc_final: 0.8016 (pm20) REVERT: M 68 ASP cc_start: 0.8952 (t0) cc_final: 0.8589 (t70) REVERT: M 145 MET cc_start: 0.7979 (tpt) cc_final: 0.7714 (tpt) REVERT: M 153 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8655 (mp) REVERT: M 381 MET cc_start: 0.8839 (mtm) cc_final: 0.8532 (mtm) REVERT: N 20 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8612 (p) REVERT: N 61 MET cc_start: 0.8306 (ptm) cc_final: 0.7898 (pmm) REVERT: N 306 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8477 (mm) REVERT: N 321 MET cc_start: 0.8616 (ptp) cc_final: 0.8376 (ptm) REVERT: H 214 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7506 (pp30) REVERT: H 278 PHE cc_start: 0.8362 (m-80) cc_final: 0.7921 (t80) REVERT: H 293 ARG cc_start: 0.8740 (mtm110) cc_final: 0.8384 (mtm-85) REVERT: A 8 GLU cc_start: 0.8134 (tp30) cc_final: 0.7906 (tp30) REVERT: A 85 LEU cc_start: 0.8440 (mt) cc_final: 0.8215 (mt) REVERT: J 64 MET cc_start: 0.9063 (mmp) cc_final: 0.8856 (mmp) REVERT: J 72 MET cc_start: 0.9116 (mtt) cc_final: 0.8843 (mmt) REVERT: J 86 GLN cc_start: 0.9005 (mm110) cc_final: 0.8685 (mm-40) REVERT: J 89 LYS cc_start: 0.8402 (mmtm) cc_final: 0.7708 (mmtt) outliers start: 130 outliers final: 86 residues processed: 570 average time/residue: 0.4700 time to fit residues: 444.9555 Evaluate side-chains 557 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 464 time to evaluate : 4.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 260 ASN Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 647 MET Chi-restraints excluded: chain G residue 867 ASN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 463 CYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 413 ASN Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 512 TRP Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 306 LEU Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 214 GLN Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 91 ASN Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 115 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 416 optimal weight: 30.0000 chunk 316 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 282 optimal weight: 10.0000 chunk 422 optimal weight: 5.9990 chunk 447 optimal weight: 7.9990 chunk 220 optimal weight: 0.9990 chunk 400 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 253 ASN G 765 GLN G 867 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN I 168 ASN L 121 ASN L 301 GLN M 348 HIS ** H 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 37519 Z= 0.743 Angle : 2.199 50.666 50989 Z= 1.446 Chirality : 0.441 6.377 5739 Planarity : 0.004 0.096 6410 Dihedral : 6.178 165.901 5154 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.99 % Allowed : 17.60 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.12), residues: 4629 helix: 1.13 (0.10), residues: 2578 sheet: -0.72 (0.29), residues: 307 loop : -1.27 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP H 73 HIS 0.005 0.001 HIS G 178 PHE 0.031 0.001 PHE L 430 TYR 0.027 0.001 TYR M 435 ARG 0.009 0.000 ARG G 804 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 483 time to evaluate : 4.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 316 LYS cc_start: 0.8904 (mtmm) cc_final: 0.8514 (mmtt) REVERT: E 37 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8513 (mt) REVERT: E 78 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.7929 (mp10) REVERT: E 93 ASP cc_start: 0.8381 (t0) cc_final: 0.7957 (t0) REVERT: G 308 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8732 (mp) REVERT: G 517 ASN cc_start: 0.8648 (m-40) cc_final: 0.8420 (m110) REVERT: G 855 ASN cc_start: 0.8596 (t0) cc_final: 0.8348 (t0) REVERT: C 62 ASP cc_start: 0.9141 (t0) cc_final: 0.8766 (t0) REVERT: C 273 ASP cc_start: 0.8664 (m-30) cc_final: 0.8310 (m-30) REVERT: C 381 ARG cc_start: 0.8600 (tpp80) cc_final: 0.8351 (tpp-160) REVERT: I 84 ASP cc_start: 0.8923 (p0) cc_final: 0.8637 (p0) REVERT: L 175 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8161 (mmm160) REVERT: L 216 MET cc_start: 0.8172 (mtt) cc_final: 0.7940 (mtt) REVERT: L 258 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8210 (ttt) REVERT: L 319 MET cc_start: 0.8631 (mmt) cc_final: 0.8244 (mmt) REVERT: L 476 GLN cc_start: 0.8554 (mp10) cc_final: 0.7974 (pm20) REVERT: M 68 ASP cc_start: 0.8965 (t0) cc_final: 0.8575 (t70) REVERT: M 153 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8676 (mp) REVERT: N 20 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8672 (p) REVERT: N 61 MET cc_start: 0.8314 (ptm) cc_final: 0.7930 (pmm) REVERT: N 198 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8113 (tt) REVERT: H 32 MET cc_start: 0.7009 (ptp) cc_final: 0.6492 (mmm) REVERT: H 278 PHE cc_start: 0.8372 (m-80) cc_final: 0.7906 (t80) REVERT: H 286 ARG cc_start: 0.8449 (mmm160) cc_final: 0.8085 (tpt-90) REVERT: H 293 ARG cc_start: 0.8708 (mtm110) cc_final: 0.8366 (mtm-85) REVERT: A 8 GLU cc_start: 0.8183 (tp30) cc_final: 0.7981 (tp30) REVERT: A 85 LEU cc_start: 0.8350 (mt) cc_final: 0.7905 (mt) REVERT: K 36 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7635 (mm-30) REVERT: J 86 GLN cc_start: 0.8931 (mm110) cc_final: 0.8696 (mm110) REVERT: J 91 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8746 (pm20) outliers start: 114 outliers final: 66 residues processed: 562 average time/residue: 0.4737 time to fit residues: 439.6207 Evaluate side-chains 542 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 467 time to evaluate : 4.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 728 GLN Chi-restraints excluded: chain G residue 765 GLN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 175 ARG Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 345 LEU Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 413 ASN Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 512 TRP Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 304 MET Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 91 GLN Chi-restraints excluded: chain J residue 115 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 372 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 333 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 381 optimal weight: 2.9990 chunk 309 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 228 optimal weight: 5.9990 chunk 401 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN I 168 ASN L 121 ASN L 301 GLN L 409 ASN ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 37519 Z= 0.744 Angle : 2.200 50.647 50989 Z= 1.447 Chirality : 0.442 6.392 5739 Planarity : 0.004 0.094 6410 Dihedral : 6.113 166.101 5152 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.51 % Allowed : 17.49 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.12), residues: 4629 helix: 1.22 (0.10), residues: 2576 sheet: -0.68 (0.29), residues: 307 loop : -1.24 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP H 73 HIS 0.004 0.001 HIS G 178 PHE 0.020 0.001 PHE L 430 TYR 0.025 0.001 TYR M 435 ARG 0.010 0.000 ARG G 804 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 476 time to evaluate : 4.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 410 SER cc_start: 0.9223 (OUTLIER) cc_final: 0.8970 (p) REVERT: E 37 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8360 (mt) REVERT: E 78 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.7905 (mp10) REVERT: E 93 ASP cc_start: 0.8392 (t0) cc_final: 0.7975 (t0) REVERT: G 308 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8749 (mp) REVERT: G 517 ASN cc_start: 0.8654 (m-40) cc_final: 0.8426 (m110) REVERT: G 855 ASN cc_start: 0.8595 (t0) cc_final: 0.8348 (t0) REVERT: C 62 ASP cc_start: 0.9141 (t0) cc_final: 0.8784 (t0) REVERT: C 273 ASP cc_start: 0.8659 (m-30) cc_final: 0.8321 (m-30) REVERT: C 381 ARG cc_start: 0.8579 (tpp80) cc_final: 0.8361 (tpp-160) REVERT: B 170 MET cc_start: 0.8781 (mmm) cc_final: 0.8508 (mmm) REVERT: I 84 ASP cc_start: 0.8884 (p0) cc_final: 0.8570 (p0) REVERT: L 175 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8168 (mmm160) REVERT: L 258 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8201 (ttt) REVERT: L 319 MET cc_start: 0.8707 (mmt) cc_final: 0.8305 (mmt) REVERT: L 476 GLN cc_start: 0.8544 (mp10) cc_final: 0.7967 (pm20) REVERT: M 68 ASP cc_start: 0.8969 (t0) cc_final: 0.8581 (t70) REVERT: M 153 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8673 (mp) REVERT: N 20 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8653 (p) REVERT: N 61 MET cc_start: 0.8326 (ptm) cc_final: 0.7939 (pmm) REVERT: N 198 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8105 (tt) REVERT: N 388 MET cc_start: 0.8751 (ptm) cc_final: 0.8472 (ptp) REVERT: H 88 MET cc_start: 0.7742 (mmt) cc_final: 0.7267 (mmt) REVERT: H 111 ASP cc_start: 0.8460 (t0) cc_final: 0.8186 (t0) REVERT: H 278 PHE cc_start: 0.8456 (m-80) cc_final: 0.7961 (t80) REVERT: H 286 ARG cc_start: 0.8567 (mmm160) cc_final: 0.8289 (tpt-90) REVERT: H 293 ARG cc_start: 0.8719 (mtm110) cc_final: 0.8459 (mtm-85) REVERT: A 85 LEU cc_start: 0.8316 (mt) cc_final: 0.7859 (mt) REVERT: K 36 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7607 (mm-30) REVERT: J 86 GLN cc_start: 0.8947 (mm110) cc_final: 0.8743 (mm110) REVERT: J 91 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8821 (pm20) outliers start: 134 outliers final: 94 residues processed: 574 average time/residue: 0.4627 time to fit residues: 440.3151 Evaluate side-chains 568 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 464 time to evaluate : 3.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 370 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 728 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 867 ASN Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 277 TYR Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 463 CYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 175 ARG Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 413 ASN Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 512 TRP Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 304 MET Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 91 GLN Chi-restraints excluded: chain J residue 115 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 150 optimal weight: 2.9990 chunk 403 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 262 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 447 optimal weight: 2.9990 chunk 371 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 37 optimal weight: 0.4980 chunk 148 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN I 168 ASN L 58 GLN L 121 ASN ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.246 37519 Z= 0.739 Angle : 2.197 50.639 50989 Z= 1.446 Chirality : 0.441 6.364 5739 Planarity : 0.004 0.093 6410 Dihedral : 6.055 165.918 5152 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.46 % Allowed : 17.75 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.13), residues: 4629 helix: 1.31 (0.10), residues: 2574 sheet: -0.59 (0.29), residues: 313 loop : -1.17 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP H 73 HIS 0.004 0.001 HIS G 178 PHE 0.018 0.001 PHE L 341 TYR 0.040 0.001 TYR M 435 ARG 0.011 0.000 ARG G 804 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 480 time to evaluate : 4.062 Fit side-chains revert: symmetry clash REVERT: F 316 LYS cc_start: 0.8890 (mtmm) cc_final: 0.8529 (mmtt) REVERT: F 410 SER cc_start: 0.9215 (OUTLIER) cc_final: 0.8967 (p) REVERT: E 78 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.7883 (mp10) REVERT: E 93 ASP cc_start: 0.8377 (t0) cc_final: 0.7954 (t0) REVERT: G 308 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8748 (mp) REVERT: G 517 ASN cc_start: 0.8631 (m-40) cc_final: 0.8408 (m110) REVERT: G 603 MET cc_start: 0.8959 (mmm) cc_final: 0.8625 (mmt) REVERT: G 670 GLN cc_start: 0.8671 (tm-30) cc_final: 0.7993 (tm-30) REVERT: G 804 ARG cc_start: 0.8287 (ttm110) cc_final: 0.7973 (ttm110) REVERT: G 855 ASN cc_start: 0.8581 (t0) cc_final: 0.8327 (t0) REVERT: C 62 ASP cc_start: 0.9132 (t0) cc_final: 0.8788 (t0) REVERT: C 273 ASP cc_start: 0.8638 (m-30) cc_final: 0.8253 (m-30) REVERT: C 381 ARG cc_start: 0.8592 (tpp80) cc_final: 0.8379 (tpp-160) REVERT: I 84 ASP cc_start: 0.8865 (p0) cc_final: 0.8622 (p0) REVERT: I 159 ASP cc_start: 0.7054 (p0) cc_final: 0.6653 (p0) REVERT: L 258 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8146 (ttt) REVERT: L 319 MET cc_start: 0.8735 (mmt) cc_final: 0.8398 (mmt) REVERT: L 476 GLN cc_start: 0.8542 (mp10) cc_final: 0.7961 (pm20) REVERT: L 512 TRP cc_start: 0.8130 (OUTLIER) cc_final: 0.7515 (t-100) REVERT: L 568 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.7550 (mmt) REVERT: M 68 ASP cc_start: 0.8966 (t0) cc_final: 0.8580 (t70) REVERT: M 153 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8662 (mp) REVERT: M 165 LYS cc_start: 0.7928 (tttt) cc_final: 0.7295 (tppt) REVERT: M 398 MET cc_start: 0.8212 (tpp) cc_final: 0.7858 (tpp) REVERT: N 20 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8660 (p) REVERT: N 61 MET cc_start: 0.8332 (ptm) cc_final: 0.7943 (pmm) REVERT: N 198 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8070 (tt) REVERT: N 321 MET cc_start: 0.8586 (ptp) cc_final: 0.8299 (ptm) REVERT: N 388 MET cc_start: 0.8743 (ptm) cc_final: 0.8499 (ptp) REVERT: H 32 MET cc_start: 0.7227 (ttp) cc_final: 0.6717 (mmt) REVERT: H 70 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7220 (tttm) REVERT: H 88 MET cc_start: 0.7760 (mmt) cc_final: 0.7271 (mmt) REVERT: H 111 ASP cc_start: 0.8444 (t0) cc_final: 0.8159 (t0) REVERT: H 278 PHE cc_start: 0.8458 (m-80) cc_final: 0.7986 (t80) REVERT: H 286 ARG cc_start: 0.8603 (mmm160) cc_final: 0.8231 (tpt-90) REVERT: H 293 ARG cc_start: 0.8669 (mtm110) cc_final: 0.8346 (mtm-85) REVERT: K 36 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7513 (mm-30) REVERT: J 72 MET cc_start: 0.9011 (mmm) cc_final: 0.8509 (mmm) REVERT: J 86 GLN cc_start: 0.8928 (mm110) cc_final: 0.8674 (mm110) REVERT: J 88 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7237 (mm) REVERT: J 89 LYS cc_start: 0.8542 (mmtm) cc_final: 0.7882 (mmtt) REVERT: J 91 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8826 (pm20) outliers start: 132 outliers final: 84 residues processed: 578 average time/residue: 0.4826 time to fit residues: 462.1683 Evaluate side-chains 564 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 468 time to evaluate : 4.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 298 ASP Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 370 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 728 GLN Chi-restraints excluded: chain G residue 867 ASN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 413 ASN Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 512 TRP Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 91 ASN Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 91 GLN Chi-restraints excluded: chain J residue 115 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 431 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 255 optimal weight: 8.9990 chunk 327 optimal weight: 2.9990 chunk 253 optimal weight: 0.8980 chunk 377 optimal weight: 6.9990 chunk 250 optimal weight: 0.9990 chunk 446 optimal weight: 7.9990 chunk 279 optimal weight: 5.9990 chunk 272 optimal weight: 20.0000 chunk 206 optimal weight: 20.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN I 168 ASN ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 37519 Z= 0.759 Angle : 2.207 50.665 50989 Z= 1.449 Chirality : 0.442 6.386 5739 Planarity : 0.004 0.094 6410 Dihedral : 6.145 166.118 5152 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.59 % Allowed : 17.60 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.13), residues: 4629 helix: 1.31 (0.10), residues: 2565 sheet: -0.59 (0.29), residues: 315 loop : -1.11 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.001 TRP H 73 HIS 0.004 0.001 HIS G 101 PHE 0.020 0.001 PHE L 341 TYR 0.030 0.001 TYR M 435 ARG 0.011 0.000 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 466 time to evaluate : 4.179 Fit side-chains revert: symmetry clash REVERT: F 316 LYS cc_start: 0.8931 (mtmm) cc_final: 0.8584 (mmtt) REVERT: F 410 SER cc_start: 0.9219 (OUTLIER) cc_final: 0.8969 (p) REVERT: E 78 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.7921 (mp10) REVERT: E 93 ASP cc_start: 0.8424 (t0) cc_final: 0.8011 (t0) REVERT: G 308 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8751 (mp) REVERT: G 517 ASN cc_start: 0.8684 (m-40) cc_final: 0.8454 (m110) REVERT: G 855 ASN cc_start: 0.8596 (t0) cc_final: 0.8363 (t0) REVERT: C 62 ASP cc_start: 0.9121 (t0) cc_final: 0.8801 (t0) REVERT: C 273 ASP cc_start: 0.8715 (m-30) cc_final: 0.8369 (m-30) REVERT: C 381 ARG cc_start: 0.8607 (tpp80) cc_final: 0.8404 (tpp-160) REVERT: I 84 ASP cc_start: 0.8904 (p0) cc_final: 0.8677 (p0) REVERT: L 258 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8199 (ttt) REVERT: L 319 MET cc_start: 0.8745 (mmt) cc_final: 0.8400 (mmt) REVERT: L 476 GLN cc_start: 0.8560 (mp10) cc_final: 0.7978 (pm20) REVERT: L 512 TRP cc_start: 0.8136 (OUTLIER) cc_final: 0.7506 (t-100) REVERT: L 568 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.7577 (mmt) REVERT: M 153 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8679 (mp) REVERT: M 165 LYS cc_start: 0.7951 (tttt) cc_final: 0.7317 (tppt) REVERT: M 299 PHE cc_start: 0.8655 (m-10) cc_final: 0.8249 (m-10) REVERT: N 20 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8611 (p) REVERT: N 61 MET cc_start: 0.8326 (ptm) cc_final: 0.7934 (pmm) REVERT: N 198 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8064 (tt) REVERT: N 321 MET cc_start: 0.8581 (ptp) cc_final: 0.8309 (ptm) REVERT: N 388 MET cc_start: 0.8694 (ptm) cc_final: 0.8452 (ptp) REVERT: H 70 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7304 (tttm) REVERT: H 88 MET cc_start: 0.7831 (mmt) cc_final: 0.7345 (mmt) REVERT: H 111 ASP cc_start: 0.8499 (t0) cc_final: 0.8207 (t0) REVERT: H 278 PHE cc_start: 0.8503 (m-80) cc_final: 0.8034 (t80) REVERT: H 286 ARG cc_start: 0.8589 (mmm160) cc_final: 0.8282 (tpt-90) REVERT: H 293 ARG cc_start: 0.8665 (mtm110) cc_final: 0.8355 (mtm-85) REVERT: A 8 GLU cc_start: 0.8104 (tp30) cc_final: 0.7885 (tp30) REVERT: K 36 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7601 (mm-30) REVERT: J 86 GLN cc_start: 0.8958 (mm110) cc_final: 0.8653 (mm110) REVERT: J 88 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7498 (mm) REVERT: J 89 LYS cc_start: 0.8639 (mmtm) cc_final: 0.7931 (mmtt) REVERT: J 91 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8881 (pm20) outliers start: 137 outliers final: 110 residues processed: 558 average time/residue: 0.4755 time to fit residues: 438.9063 Evaluate side-chains 575 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 453 time to evaluate : 4.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 298 ASP Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 105 CYS Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 370 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 647 MET Chi-restraints excluded: chain G residue 728 GLN Chi-restraints excluded: chain G residue 730 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 867 ASN Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 463 CYS Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 592 ASP Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 413 ASN Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 512 TRP Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 91 GLN Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 120 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 276 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 266 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 283 optimal weight: 10.0000 chunk 304 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 350 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 HIS E 114 ASN G 283 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN L 58 GLN ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 37519 Z= 0.749 Angle : 2.204 50.653 50989 Z= 1.448 Chirality : 0.442 6.375 5739 Planarity : 0.004 0.093 6410 Dihedral : 6.139 165.742 5152 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.61 % Allowed : 17.67 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.13), residues: 4629 helix: 1.34 (0.10), residues: 2579 sheet: -0.56 (0.29), residues: 313 loop : -1.12 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 87 HIS 0.004 0.001 HIS G 178 PHE 0.022 0.001 PHE L 430 TYR 0.029 0.001 TYR M 435 ARG 0.013 0.000 ARG G 804 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 461 time to evaluate : 4.062 Fit side-chains revert: symmetry clash REVERT: F 316 LYS cc_start: 0.8952 (mtmm) cc_final: 0.8606 (mmtt) REVERT: F 410 SER cc_start: 0.9221 (OUTLIER) cc_final: 0.8980 (p) REVERT: E 78 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.7911 (mp10) REVERT: E 93 ASP cc_start: 0.8423 (t0) cc_final: 0.8062 (t0) REVERT: G 308 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8757 (mp) REVERT: G 804 ARG cc_start: 0.8303 (ttm110) cc_final: 0.7981 (ttm110) REVERT: G 855 ASN cc_start: 0.8591 (t0) cc_final: 0.8351 (t0) REVERT: C 62 ASP cc_start: 0.9128 (t0) cc_final: 0.8819 (t0) REVERT: C 273 ASP cc_start: 0.8704 (m-30) cc_final: 0.8369 (m-30) REVERT: C 381 ARG cc_start: 0.8607 (tpp80) cc_final: 0.8403 (tpp-160) REVERT: L 258 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8187 (ttt) REVERT: L 319 MET cc_start: 0.8770 (mmt) cc_final: 0.8448 (mmt) REVERT: L 476 GLN cc_start: 0.8542 (mp10) cc_final: 0.7961 (pm20) REVERT: L 512 TRP cc_start: 0.8144 (OUTLIER) cc_final: 0.7518 (t-100) REVERT: L 568 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.7568 (mmt) REVERT: M 153 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8673 (mp) REVERT: M 165 LYS cc_start: 0.7944 (tttt) cc_final: 0.7319 (tppt) REVERT: M 299 PHE cc_start: 0.8665 (m-10) cc_final: 0.8266 (m-10) REVERT: N 20 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8616 (p) REVERT: N 61 MET cc_start: 0.8318 (ptm) cc_final: 0.7918 (pmm) REVERT: N 198 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8041 (tt) REVERT: N 321 MET cc_start: 0.8554 (ptp) cc_final: 0.8283 (ptm) REVERT: N 388 MET cc_start: 0.8688 (ptm) cc_final: 0.8443 (ptp) REVERT: H 70 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7353 (tttm) REVERT: H 88 MET cc_start: 0.7859 (mmt) cc_final: 0.7382 (mmt) REVERT: H 278 PHE cc_start: 0.8480 (m-80) cc_final: 0.8004 (t80) REVERT: H 293 ARG cc_start: 0.8640 (mtm110) cc_final: 0.8325 (mtm-85) REVERT: A 8 GLU cc_start: 0.8121 (tp30) cc_final: 0.7886 (tp30) REVERT: K 36 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7581 (mm-30) REVERT: J 72 MET cc_start: 0.9048 (mmm) cc_final: 0.8647 (mtm) REVERT: J 86 GLN cc_start: 0.8965 (mm110) cc_final: 0.8717 (mm110) REVERT: J 88 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7515 (mm) REVERT: J 89 LYS cc_start: 0.8630 (mmtm) cc_final: 0.8006 (mmtt) REVERT: J 91 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8824 (pm20) outliers start: 138 outliers final: 110 residues processed: 557 average time/residue: 0.4855 time to fit residues: 450.4257 Evaluate side-chains 572 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 450 time to evaluate : 3.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 298 ASP Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 105 CYS Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 370 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 728 GLN Chi-restraints excluded: chain G residue 730 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 867 ASN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 463 CYS Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 413 ASN Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 512 TRP Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 91 GLN Chi-restraints excluded: chain J residue 115 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 405 optimal weight: 7.9990 chunk 427 optimal weight: 0.9980 chunk 390 optimal weight: 0.9990 chunk 415 optimal weight: 10.0000 chunk 250 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 326 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 375 optimal weight: 8.9990 chunk 393 optimal weight: 2.9990 chunk 414 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN G 517 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 37519 Z= 0.757 Angle : 2.210 50.663 50989 Z= 1.450 Chirality : 0.442 6.383 5739 Planarity : 0.004 0.094 6410 Dihedral : 6.199 165.789 5152 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.69 % Allowed : 17.70 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.13), residues: 4629 helix: 1.35 (0.10), residues: 2565 sheet: -0.58 (0.29), residues: 315 loop : -1.09 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP H 73 HIS 0.004 0.001 HIS G 101 PHE 0.026 0.001 PHE A 74 TYR 0.027 0.001 TYR M 435 ARG 0.012 0.000 ARG G 804 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 454 time to evaluate : 4.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 410 SER cc_start: 0.9219 (OUTLIER) cc_final: 0.8953 (p) REVERT: E 78 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.7912 (mp10) REVERT: E 93 ASP cc_start: 0.8443 (t0) cc_final: 0.8093 (t0) REVERT: G 308 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8741 (mp) REVERT: G 804 ARG cc_start: 0.8307 (ttm110) cc_final: 0.8000 (ttm110) REVERT: G 855 ASN cc_start: 0.8606 (t0) cc_final: 0.8376 (t0) REVERT: C 62 ASP cc_start: 0.9142 (t0) cc_final: 0.8767 (t0) REVERT: C 273 ASP cc_start: 0.8732 (m-30) cc_final: 0.8372 (m-30) REVERT: C 381 ARG cc_start: 0.8640 (tpp80) cc_final: 0.8439 (tpp-160) REVERT: L 258 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8194 (ttt) REVERT: L 319 MET cc_start: 0.8760 (mmt) cc_final: 0.8427 (mmt) REVERT: L 476 GLN cc_start: 0.8570 (mp10) cc_final: 0.7992 (pm20) REVERT: L 512 TRP cc_start: 0.8124 (OUTLIER) cc_final: 0.7438 (t-100) REVERT: L 568 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.7597 (mmt) REVERT: M 153 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8669 (mp) REVERT: M 165 LYS cc_start: 0.7952 (tttt) cc_final: 0.7330 (tppt) REVERT: M 299 PHE cc_start: 0.8675 (m-10) cc_final: 0.8276 (m-10) REVERT: N 20 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8618 (p) REVERT: N 61 MET cc_start: 0.8313 (ptm) cc_final: 0.7910 (pmm) REVERT: N 198 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8055 (tt) REVERT: N 321 MET cc_start: 0.8558 (ptp) cc_final: 0.8285 (ptm) REVERT: N 388 MET cc_start: 0.8765 (ptm) cc_final: 0.8509 (ptp) REVERT: H 64 MET cc_start: 0.8361 (tpt) cc_final: 0.8109 (tpt) REVERT: H 70 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7373 (tttm) REVERT: H 88 MET cc_start: 0.7912 (mmt) cc_final: 0.7428 (mmt) REVERT: H 293 ARG cc_start: 0.8684 (mtm110) cc_final: 0.8329 (mtm-85) REVERT: A 8 GLU cc_start: 0.8107 (tp30) cc_final: 0.7897 (tp30) REVERT: K 36 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7635 (mm-30) REVERT: J 72 MET cc_start: 0.8998 (mmm) cc_final: 0.8571 (mtm) REVERT: J 86 GLN cc_start: 0.8950 (mm110) cc_final: 0.8711 (mm110) REVERT: J 89 LYS cc_start: 0.8684 (mmtm) cc_final: 0.8394 (mmtt) REVERT: J 91 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8850 (pm20) outliers start: 141 outliers final: 112 residues processed: 553 average time/residue: 0.4825 time to fit residues: 440.3401 Evaluate side-chains 571 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 448 time to evaluate : 4.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 298 ASP Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 105 CYS Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 647 MET Chi-restraints excluded: chain G residue 728 GLN Chi-restraints excluded: chain G residue 730 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 867 ASN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 463 CYS Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 592 ASP Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 413 ASN Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 512 TRP Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 91 GLN Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 120 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 273 optimal weight: 2.9990 chunk 439 optimal weight: 5.9990 chunk 268 optimal weight: 10.0000 chunk 208 optimal weight: 30.0000 chunk 305 optimal weight: 10.0000 chunk 461 optimal weight: 5.9990 chunk 424 optimal weight: 6.9990 chunk 367 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 283 optimal weight: 5.9990 chunk 225 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 HIS ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 37519 Z= 0.759 Angle : 2.212 50.676 50989 Z= 1.451 Chirality : 0.442 6.383 5739 Planarity : 0.004 0.093 6410 Dihedral : 6.221 165.600 5152 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.59 % Allowed : 17.78 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.13), residues: 4629 helix: 1.32 (0.10), residues: 2577 sheet: -0.58 (0.29), residues: 315 loop : -1.11 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 386 HIS 0.004 0.001 HIS G 101 PHE 0.027 0.001 PHE L 430 TYR 0.026 0.001 TYR M 435 ARG 0.011 0.000 ARG G 804 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 451 time to evaluate : 3.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 387 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8507 (mp) REVERT: F 410 SER cc_start: 0.9222 (OUTLIER) cc_final: 0.8966 (p) REVERT: E 37 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8335 (mt) REVERT: E 78 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7907 (mp10) REVERT: E 93 ASP cc_start: 0.8445 (t0) cc_final: 0.8100 (t0) REVERT: G 308 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8736 (mp) REVERT: G 804 ARG cc_start: 0.8313 (ttm110) cc_final: 0.8011 (ttm110) REVERT: G 855 ASN cc_start: 0.8609 (t0) cc_final: 0.8146 (p0) REVERT: C 62 ASP cc_start: 0.9148 (t0) cc_final: 0.8785 (t0) REVERT: C 273 ASP cc_start: 0.8759 (m-30) cc_final: 0.8423 (m-30) REVERT: C 381 ARG cc_start: 0.8645 (tpp80) cc_final: 0.8442 (tpp-160) REVERT: L 258 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8205 (ttt) REVERT: L 319 MET cc_start: 0.8771 (mmt) cc_final: 0.8447 (mmt) REVERT: L 326 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8354 (mp10) REVERT: L 476 GLN cc_start: 0.8548 (mp10) cc_final: 0.7955 (pm20) REVERT: L 512 TRP cc_start: 0.8170 (OUTLIER) cc_final: 0.7555 (t-100) REVERT: L 568 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.7625 (mmt) REVERT: M 56 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8384 (mm-40) REVERT: M 153 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8649 (mp) REVERT: M 165 LYS cc_start: 0.7951 (tttt) cc_final: 0.7334 (tppt) REVERT: M 299 PHE cc_start: 0.8702 (m-10) cc_final: 0.8322 (m-10) REVERT: N 20 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8622 (p) REVERT: N 61 MET cc_start: 0.8325 (ptm) cc_final: 0.7903 (pmm) REVERT: N 198 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8062 (tt) REVERT: N 321 MET cc_start: 0.8590 (ptp) cc_final: 0.8325 (ptm) REVERT: N 388 MET cc_start: 0.8758 (ptm) cc_final: 0.8512 (ptp) REVERT: H 36 GLU cc_start: 0.8424 (tt0) cc_final: 0.8076 (tt0) REVERT: H 64 MET cc_start: 0.8360 (tpt) cc_final: 0.8131 (tpt) REVERT: H 70 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7427 (tttm) REVERT: H 88 MET cc_start: 0.7961 (mmt) cc_final: 0.7473 (mmt) REVERT: H 214 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7313 (pp30) REVERT: H 242 TYR cc_start: 0.8815 (m-10) cc_final: 0.8589 (m-10) REVERT: H 293 ARG cc_start: 0.8662 (mtm110) cc_final: 0.8305 (mtm-85) REVERT: A 8 GLU cc_start: 0.8124 (tp30) cc_final: 0.7915 (tp30) REVERT: K 36 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7627 (mm-30) REVERT: J 72 MET cc_start: 0.9000 (mmm) cc_final: 0.8540 (mtm) REVERT: J 86 GLN cc_start: 0.9000 (mm110) cc_final: 0.8773 (mm110) outliers start: 137 outliers final: 108 residues processed: 547 average time/residue: 0.4850 time to fit residues: 440.1435 Evaluate side-chains 572 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 450 time to evaluate : 4.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 298 ASP Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 105 CYS Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 237 CYS Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 647 MET Chi-restraints excluded: chain G residue 728 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 867 ASN Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 463 CYS Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 592 ASP Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 326 GLN Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain L residue 413 ASN Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 512 TRP Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 214 GLN Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 115 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 291 optimal weight: 0.9980 chunk 391 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 338 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 367 optimal weight: 0.6980 chunk 153 optimal weight: 9.9990 chunk 377 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN L 58 GLN ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.070948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.057622 restraints weight = 76613.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.059225 restraints weight = 45866.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.060310 restraints weight = 32949.062| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 37519 Z= 0.744 Angle : 2.206 50.639 50989 Z= 1.449 Chirality : 0.442 6.369 5739 Planarity : 0.004 0.092 6410 Dihedral : 6.153 165.346 5152 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.19 % Allowed : 18.15 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.13), residues: 4629 helix: 1.37 (0.10), residues: 2582 sheet: -0.61 (0.30), residues: 300 loop : -1.11 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP H 73 HIS 0.004 0.001 HIS G 101 PHE 0.027 0.001 PHE L 430 TYR 0.029 0.001 TYR M 435 ARG 0.011 0.000 ARG G 804 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8293.78 seconds wall clock time: 151 minutes 2.87 seconds (9062.87 seconds total)