Starting phenix.real_space_refine (version: dev) on Tue Dec 20 16:02:10 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7s_14536/12_2022/7z7s_14536_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7s_14536/12_2022/7z7s_14536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7s_14536/12_2022/7z7s_14536.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7s_14536/12_2022/7z7s_14536.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7s_14536/12_2022/7z7s_14536_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7s_14536/12_2022/7z7s_14536_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.024 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "F GLU 49": "OE1" <-> "OE2" Residue "F GLU 138": "OE1" <-> "OE2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F GLU 183": "OE1" <-> "OE2" Residue "F GLU 275": "OE1" <-> "OE2" Residue "F GLU 420": "OE1" <-> "OE2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "E ASP 148": "OD1" <-> "OD2" Residue "G ASP 438": "OD1" <-> "OD2" Residue "G ASP 528": "OD1" <-> "OD2" Residue "G GLU 665": "OE1" <-> "OE2" Residue "G GLU 792": "OE1" <-> "OE2" Residue "G PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C ASP 273": "OD1" <-> "OD2" Residue "C ASP 462": "OD1" <-> "OD2" Residue "C GLU 490": "OE1" <-> "OE2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B ASP 189": "OD1" <-> "OD2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "I GLU 147": "OE1" <-> "OE2" Residue "I ASP 159": "OD1" <-> "OD2" Residue "H TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 218": "OE1" <-> "OE2" Residue "H GLU 241": "OE1" <-> "OE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "L PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 111": "OE1" <-> "OE2" Residue "L ASP 160": "OD1" <-> "OD2" Residue "L ASP 178": "OD1" <-> "OD2" Residue "L TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 329": "OD1" <-> "OD2" Residue "L GLU 401": "OE1" <-> "OE2" Residue "M TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 84": "OD1" <-> "OD2" Residue "M PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 246": "OD1" <-> "OD2" Residue "M GLU 285": "OE1" <-> "OE2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N GLU 133": "OE1" <-> "OE2" Residue "N GLU 200": "OE1" <-> "OE2" Residue "N TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 55": "OE1" <-> "OE2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 120": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 39208 Number of models: 1 Model: "" Number of chains: 37 Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 7017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7017 Classifications: {'peptide': 905} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 41, 'TRANS': 863} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 4760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4760 Classifications: {'peptide': 589} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 551} Chain: "B" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1693 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Chain: "I" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1436 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 166} Chain: "H" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2534 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 306} Chain: "A" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1037 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "L" Number of atoms: 4558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4558 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 579} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 482} Chain: "N" Number of atoms: 3601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3601 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 454} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 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: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'3PE': 1, 'DCQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'DCQ': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 55 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "H" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "L" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 217 Unusual residues: {'3PE': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "M" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "N" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'3PE': 1, 'LFA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "J" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "F" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "G" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 353 Classifications: {'water': 353} Link IDs: {None: 352} Chain: "C" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 206 Classifications: {'water': 206} Link IDs: {None: 205} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "I" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "H" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "L" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "M" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "N" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "K" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "J" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 73.008 61.008 190.032 1.00 10.28 S ATOM 2741 SG CYS F 357 76.234 60.572 194.427 1.00 13.76 S ATOM 3062 SG CYS F 398 70.497 57.112 194.878 1.00 20.39 S ATOM 2697 SG CYS F 351 75.073 54.627 191.425 1.00 9.57 S ATOM 4054 SG CYS E 92 83.146 53.375 211.387 1.00 22.13 S ATOM 4088 SG CYS E 97 83.181 54.011 214.921 1.00 21.77 S ATOM 4366 SG CYS E 133 77.962 52.650 210.916 1.00 33.26 S ATOM 4392 SG CYS E 137 77.081 53.384 214.127 1.00 34.35 S ATOM 5472 SG CYS G 114 83.693 66.810 172.593 1.00 18.98 S ATOM 5412 SG CYS G 105 88.820 70.833 174.077 1.00 26.30 S ATOM 5432 SG CYS G 108 89.624 64.686 172.104 1.00 15.17 S ATOM 5826 SG CYS G 156 77.956 59.074 177.587 1.00 31.65 S ATOM 5807 SG CYS G 153 83.748 58.027 180.776 1.00 11.11 S ATOM 5855 SG CYS G 159 81.032 53.418 177.225 1.00 8.58 S ATOM 6203 SG CYS G 203 83.085 58.553 174.047 1.00 14.69 S ATOM 6428 SG CYS G 230 80.336 49.681 153.065 1.00 18.19 S ATOM 6713 SG CYS G 265 80.174 45.972 158.417 1.00 13.70 S ATOM 6476 SG CYS G 237 74.900 49.336 156.068 1.00 17.42 S ATOM 6452 SG CYS G 233 77.259 43.965 153.091 1.00 15.96 S ATOM 4877 SG CYS G 36 71.454 60.004 180.214 1.00 9.07 S ATOM 4953 SG CYS G 47 72.999 63.443 180.586 1.00 10.32 S ATOM 4979 SG CYS G 50 67.273 65.016 180.242 1.00 16.11 S ATOM 5124 SG CYS G 69 66.746 61.423 179.981 1.00 17.16 S ATOM 17375 SG CYS B 129 93.858 93.730 148.704 1.00 12.15 S ATOM 16872 SG CYS B 64 99.051 97.647 150.215 1.00 8.28 S ATOM 16866 SG CYS B 63 93.442 99.648 152.066 1.00 13.36 S ATOM 17592 SG CYS B 158 95.672 93.802 154.332 1.00 13.04 S ATOM 18923 SG CYS I 102 94.403 88.050 160.484 1.00 13.27 S ATOM 18898 SG CYS I 99 99.999 86.767 156.959 1.00 14.68 S ATOM 18941 SG CYS I 105 98.433 83.577 162.420 1.00 22.40 S ATOM 18656 SG CYS I 70 94.637 82.775 157.192 1.00 29.28 S ATOM 18970 SG CYS I 109 99.385 78.229 168.776 1.00 10.56 S ATOM 18633 SG CYS I 66 97.559 77.383 162.613 1.00 12.18 S ATOM 18593 SG CYS I 60 101.716 73.180 164.984 1.00 11.51 S ATOM 18611 SG CYS I 63 95.403 73.685 167.373 1.00 13.63 S Time building chain proxies: 22.10, per 1000 atoms: 0.56 Number of scatterers: 39208 At special positions: 0 Unit cell: (157, 217.5, 241, 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 268 16.00 P 16 15.00 O 7871 8.00 N 6274 7.00 C 24746 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: 17.01 Conformation dependent library (CDL) restraints added in 5.3 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=" FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb=" FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1004 " pdb=" FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb=" FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb=" FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb=" FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb=" FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb=" FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb=" FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb=" FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb=" FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb=" FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb=" FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb=" FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb=" FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb=" FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb=" 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=" FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb=" FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb=" FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" SF4 G1003 " pdb=" FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb=" FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb=" FE3 SF4 G1003 " - pdb=" SG CYS G 237 " 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 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 201 helices and 27 sheets defined 54.9% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 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 57 Processing helix chain 'F' and resid 69 through 75 Processing helix chain 'F' and resid 100 through 107 removed outlier: 3.584A pdb=" N GLN F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 178 through 181 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 219 through 231 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 270 through 275 Processing helix chain 'F' and resid 302 through 306 removed outlier: 4.188A pdb=" N ASP F 306 " --> pdb=" O ALA F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 316 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 355 through 372 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 422 removed outlier: 3.938A pdb=" N GLY F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.924A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.750A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.070A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 158 through 162 Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 115 through 123 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 196 through 202 Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 220 through 222 No H-bonds generated for 'chain 'G' and resid 220 through 222' Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 272 through 276 Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 369 through 373 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 409 removed outlier: 4.613A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 424 Processing helix chain 'G' and resid 440 through 443 removed outlier: 4.312A pdb=" N ASP G 443 " --> pdb=" O ARG G 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 440 through 443' Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 509 through 524 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 559 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 601 through 604 removed outlier: 3.520A pdb=" N GLU G 604 " --> pdb=" O ALA G 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 601 through 604' Processing helix chain 'G' and resid 615 through 617 No H-bonds generated for 'chain 'G' and resid 615 through 617' Processing helix chain 'G' and resid 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 689 removed outlier: 4.921A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 764 through 770 Processing helix chain 'G' and resid 825 through 828 No H-bonds generated for 'chain 'G' and resid 825 through 828' Processing helix chain 'G' and resid 831 through 836 removed outlier: 4.033A pdb=" N SER G 835 " --> pdb=" O VAL G 832 " (cutoff:3.500A) Processing helix chain 'G' and resid 846 through 851 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 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 54 through 65 removed outlier: 5.071A pdb=" N LEU C 58 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.588A pdb=" N ASN C 135 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP C 136 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP C 142 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE C 145 " --> pdb=" O TRP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 187 through 197 Processing helix chain 'C' and resid 201 through 204 Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 280 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 330 Processing helix chain 'C' and resid 335 through 354 Processing helix chain 'C' and resid 376 through 397 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 431 Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 523 Processing helix chain 'C' and resid 564 through 576 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 591 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 39 through 51 Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 104 through 116 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 162 through 178 removed outlier: 3.715A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 4.876A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 25 removed outlier: 4.171A pdb=" N PHE I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 127 through 130 Processing helix chain 'I' and resid 134 through 136 No H-bonds generated for 'chain 'I' and resid 134 through 136' Processing helix chain 'H' and resid 6 through 43 Processing helix chain 'H' and resid 54 through 56 No H-bonds generated for 'chain 'H' and resid 54 through 56' Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 5.178A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU H 95 " --> pdb=" O PHE H 91 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 4.077A pdb=" N VAL H 127 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER H 136 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 156 Processing helix chain 'H' and resid 160 through 171 removed outlier: 4.160A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.964A 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 218 through 221 No H-bonds generated for 'chain 'H' and resid 218 through 221' Processing helix chain 'H' and resid 224 through 226 No H-bonds generated for 'chain 'H' and resid 224 through 226' Processing helix chain 'H' and resid 231 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 303 Processing helix chain 'H' and resid 305 through 322 Processing helix chain 'A' and resid 8 through 36 Processing helix chain 'A' and resid 69 through 119 removed outlier: 3.704A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 92 " --> pdb=" O TRP A 88 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'L' and resid 2 through 21 removed outlier: 4.554A pdb=" N ALA L 5 " --> pdb=" O ASN L 2 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR L 7 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU L 10 " --> pdb=" O THR L 7 " (cutoff:3.500A) Proline residue: L 11 - end of helix removed outlier: 3.550A pdb=" N LEU L 17 " --> pdb=" O GLY L 14 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER L 21 " --> pdb=" O LEU L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 55 removed outlier: 3.504A pdb=" N ASN L 55 " --> pdb=" O ASP L 51 " (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 192 Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 214 through 229 Processing helix chain 'L' and resid 237 through 242 removed outlier: 4.219A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 255 Processing helix chain 'L' and resid 260 through 268 Processing helix chain 'L' and resid 270 through 275 Processing helix chain 'L' and resid 277 through 300 removed outlier: 4.012A pdb=" N VAL L 300 " --> pdb=" O PHE L 296 " (cutoff:3.500A) Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 355 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 413 through 437 Processing helix chain 'L' and resid 455 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 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 548 removed outlier: 6.158A pdb=" N ASP L 542 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL L 548 " --> pdb=" O TYR L 545 " (cutoff:3.500A) Processing helix chain 'L' and resid 550 through 560 Processing helix chain 'L' and resid 564 through 586 Proline residue: L 572 - end of helix removed outlier: 3.666A pdb=" N LEU L 585 " --> pdb=" O LYS L 581 " (cutoff:3.500A) removed outlier: 4.312A 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: 3.599A pdb=" N GLU M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 50 Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 157 removed outlier: 4.679A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Proline residue: M 149 - end of helix Processing helix chain 'M' and resid 164 through 199 Processing helix chain 'M' and resid 207 through 211 Processing helix chain 'M' and resid 219 through 234 Processing helix chain 'M' and resid 242 through 249 removed outlier: 4.338A 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 266 through 273 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 332 removed outlier: 3.653A pdb=" N TYR M 331 " --> pdb=" O LEU M 327 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR M 332 " --> pdb=" O ILE M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 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 443 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 488 Processing helix chain 'M' and resid 490 through 502 Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 34 through 58 removed outlier: 4.595A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.266A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 120 removed outlier: 3.747A pdb=" N LEU N 107 " --> pdb=" O ASP N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 181 Processing helix chain 'N' and resid 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 226 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.319A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 removed outlier: 3.596A 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 267 through 287 Processing helix chain 'N' and resid 294 through 316 removed outlier: 3.685A pdb=" N ALA N 315 " --> pdb=" O VAL N 311 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU N 316 " --> pdb=" O ALA N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 322 through 347 Processing helix chain 'N' and resid 359 through 362 No H-bonds generated for 'chain 'N' and resid 359 through 362' Processing helix chain 'N' and resid 365 through 367 No H-bonds generated for 'chain 'N' and resid 365 through 367' Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.237A 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 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 53 Processing helix chain 'K' and resid 57 through 87 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 73 removed outlier: 3.755A pdb=" N GLY J 61 " --> pdb=" O ILE J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 87 Processing helix chain 'J' and resid 90 through 112 Proline residue: J 96 - end of helix removed outlier: 4.173A pdb=" N LEU J 99 " --> pdb=" O GLY J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 158 Processing sheet with id= A, first strand: chain 'F' and resid 213 through 218 removed outlier: 6.586A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N HIS F 172 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 260 through 265 removed outlier: 3.640A pdb=" N PHE F 252 " --> pdb=" O GLY F 260 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 87 through 92 Processing sheet with id= D, first strand: chain 'E' and resid 143 through 145 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: 6.555A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.429A 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: 6.459A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.650A 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: 6.526A pdb=" N MET G 593 " --> pdb=" O VAL G 568 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.766A 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: 6.325A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL G 379 " --> pdb=" O PRO G 430 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE G 432 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TYR G 449 " --> pdb=" O ASN G 435 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 620 through 623 Processing sheet with id= N, first strand: chain 'G' and resid 813 through 817 Processing sheet with id= O, first strand: chain 'G' and resid 859 through 863 Processing sheet with id= P, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.257A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.694A 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: 6.394A 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: 3.738A pdb=" N ASP C 244 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ILE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 531 through 538 Processing sheet with id= T, first strand: chain 'B' and resid 20 through 25 Processing sheet with id= U, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.369A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL B 153 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'I' and resid 48 through 50 Processing sheet with id= W, first strand: chain 'I' and resid 75 through 81 removed outlier: 4.034A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 68 through 70 Processing sheet with id= Y, first strand: chain 'L' and resid 60 through 66 removed outlier: 7.104A pdb=" N PHE L 77 " --> pdb=" O LEU L 64 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.854A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'N' and resid 61 through 63 1900 hydrogen bonds defined for protein. 5361 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: 14.84 Time building geometry restraints manager: 18.18 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: 16139 1.42 - 1.64: 22323 1.64 - 1.86: 411 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 38965 Sorted by residual: bond pdb=" O5D NAI F 503 " pdb=" PN NAI F 503 " ideal model delta sigma weight residual 1.650 1.586 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O13 3PE H 602 " pdb=" P 3PE H 602 " ideal model delta sigma weight residual 1.654 1.593 0.061 2.00e-02 2.50e+03 9.41e+00 bond pdb=" O13 3PE C 701 " pdb=" P 3PE C 701 " ideal model delta sigma weight residual 1.654 1.593 0.061 2.00e-02 2.50e+03 9.37e+00 bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.593 0.061 2.00e-02 2.50e+03 9.15e+00 bond pdb=" O13 3PE L 802 " pdb=" P 3PE L 802 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 9.00e+00 ... (remaining 38960 not shown) Histogram of bond angle deviations from ideal: 68.50 - 81.95: 88 81.95 - 95.41: 0 95.41 - 108.87: 2679 108.87 - 122.32: 44768 122.32 - 135.78: 5290 Bond angle restraints: 52825 Sorted by residual: angle pdb=" CA VAL K 95 " pdb=" CB VAL K 95 " pdb=" CG1 VAL K 95 " ideal model delta sigma weight residual 110.40 119.60 -9.20 1.70e+00 3.46e-01 2.93e+01 angle pdb=" CB MET H 232 " pdb=" CG MET H 232 " pdb=" SD MET H 232 " ideal model delta sigma weight residual 112.70 128.06 -15.36 3.00e+00 1.11e-01 2.62e+01 angle pdb=" CB LYS L 162 " pdb=" CG LYS L 162 " pdb=" CD LYS L 162 " ideal model delta sigma weight residual 111.30 122.55 -11.25 2.30e+00 1.89e-01 2.39e+01 angle pdb=" C ILE N 3 " pdb=" N THR N 4 " pdb=" CA THR N 4 " ideal model delta sigma weight residual 120.68 127.83 -7.15 1.52e+00 4.33e-01 2.21e+01 angle pdb=" S3 SF4 F 501 " pdb=" FE1 SF4 F 501 " pdb=" S4 SF4 F 501 " ideal model delta sigma weight residual 104.10 110.96 -6.86 1.50e+00 4.44e-01 2.09e+01 ... (remaining 52820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 22055 34.50 - 69.00: 725 69.00 - 103.51: 56 103.51 - 138.01: 0 138.01 - 172.51: 1 Dihedral angle restraints: 22837 sinusoidal: 9197 harmonic: 13640 Sorted by residual: 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 85.08 172.51 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" CA ALA G 177 " pdb=" C ALA G 177 " pdb=" N HIS G 178 " pdb=" CA HIS G 178 " ideal model delta harmonic sigma weight residual -180.00 -149.80 -30.20 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA LYS C 69 " pdb=" C LYS C 69 " pdb=" N PRO C 70 " pdb=" CA PRO C 70 " ideal model delta harmonic sigma weight residual -180.00 -151.66 -28.34 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 22834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.245: 5839 4.245 - 8.490: 0 8.490 - 12.736: 0 12.736 - 16.981: 0 16.981 - 21.226: 28 Chirality restraints: 5867 Sorted by residual: chirality pdb=" FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.67 -21.23 2.00e-01 2.50e+01 1.13e+04 chirality pdb=" FE1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " pdb=" S4 SF4 G1002 " both_signs ideal model delta sigma weight residual False -10.55 10.66 -21.22 2.00e-01 2.50e+01 1.13e+04 chirality pdb=" FE4 SF4 F 501 " pdb=" S1 SF4 F 501 " pdb=" S2 SF4 F 501 " pdb=" S3 SF4 F 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.65 21.21 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5864 not shown) Planarity restraints: 6594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ C 702 " -0.029 2.00e-02 2.50e+03 5.53e-02 9.17e+01 pdb=" C1M DCQ C 702 " -0.086 2.00e-02 2.50e+03 pdb=" C2 DCQ C 702 " -0.007 2.00e-02 2.50e+03 pdb=" C3 DCQ C 702 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DCQ C 702 " -0.014 2.00e-02 2.50e+03 pdb=" C5 DCQ C 702 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DCQ C 702 " 0.038 2.00e-02 2.50e+03 pdb=" C7 DCQ C 702 " 0.097 2.00e-02 2.50e+03 pdb=" O2 DCQ C 702 " -0.004 2.00e-02 2.50e+03 pdb=" O3 DCQ C 702 " 0.100 2.00e-02 2.50e+03 pdb=" O4 DCQ C 702 " -0.081 2.00e-02 2.50e+03 pdb=" O5 DCQ C 702 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 DCQ B 302 " -0.018 2.00e-02 2.50e+03 2.67e-02 2.13e+01 pdb=" C1M DCQ B 302 " -0.049 2.00e-02 2.50e+03 pdb=" C2 DCQ B 302 " 0.001 2.00e-02 2.50e+03 pdb=" C3 DCQ B 302 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DCQ B 302 " -0.014 2.00e-02 2.50e+03 pdb=" C5 DCQ B 302 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DCQ B 302 " 0.015 2.00e-02 2.50e+03 pdb=" C7 DCQ B 302 " 0.058 2.00e-02 2.50e+03 pdb=" O2 DCQ B 302 " 0.015 2.00e-02 2.50e+03 pdb=" O3 DCQ B 302 " 0.033 2.00e-02 2.50e+03 pdb=" O4 DCQ B 302 " -0.016 2.00e-02 2.50e+03 pdb=" O5 DCQ B 302 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER G 763 " -0.044 5.00e-02 4.00e+02 6.57e-02 6.92e+00 pdb=" N PRO G 764 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO G 764 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 764 " -0.036 5.00e-02 4.00e+02 ... (remaining 6591 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 6285 2.76 - 3.29: 38243 3.29 - 3.83: 77311 3.83 - 4.36: 94570 4.36 - 4.90: 151660 Nonbonded interactions: 368069 Sorted by model distance: nonbonded pdb=" OD1 ASN C 223 " pdb=" OH TYR B 57 " model vdw 2.219 2.440 nonbonded pdb=" OE2 GLU I 169 " pdb=" O HOH I 301 " model vdw 2.230 2.440 nonbonded pdb=" OD2 ASP C 342 " pdb=" OH TYR C 394 " model vdw 2.237 2.440 nonbonded pdb=" OG1 THR C 334 " pdb=" O ALA H 287 " model vdw 2.238 2.440 nonbonded pdb=" O TYR E 76 " pdb=" O HOH E 301 " model vdw 2.244 2.440 ... (remaining 368064 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 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 16 5.49 5 S 268 5.16 5 C 24746 2.51 5 N 6274 2.21 5 O 7871 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 18.170 Check model and map are aligned: 0.600 Convert atoms to be neutral: 0.380 Process input model: 107.540 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9204 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 : 0.007 0.080 38965 Z= 0.435 Angle : 0.811 15.356 52825 Z= 0.418 Chirality : 1.462 21.226 5867 Planarity : 0.006 0.073 6594 Dihedral : 16.334 172.509 14113 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.26 % Favored : 97.66 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.11), residues: 4740 helix: 0.47 (0.09), residues: 2694 sheet: -0.39 (0.28), residues: 319 loop : -0.56 (0.14), residues: 1727 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 536 time to evaluate : 4.307 Fit side-chains outliers start: 65 outliers final: 40 residues processed: 589 average time/residue: 1.6289 time to fit residues: 1159.9982 Evaluate side-chains 560 residues out of total 3905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 520 time to evaluate : 4.872 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 35 residues processed: 5 average time/residue: 0.6832 time to fit residues: 11.1485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 398 optimal weight: 10.0000 chunk 357 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 241 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 369 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 224 optimal weight: 9.9990 chunk 275 optimal weight: 6.9990 chunk 428 optimal weight: 9.9990 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 53 GLN E 82 GLN G 655 HIS G 845 ASN C 31 ASN C 190 GLN C 319 HIS H 323 GLN M 179 GLN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 403 ASN N 447 ASN K 88 GLN J 75 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9176 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.267 38965 Z= 0.776 Angle : 2.167 50.658 52825 Z= 1.422 Chirality : 0.449 6.727 5867 Planarity : 0.005 0.054 6594 Dihedral : 7.951 173.712 5644 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.98 % Favored : 97.95 % Rotamer Outliers : 3.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.12), residues: 4740 helix: 1.14 (0.10), residues: 2675 sheet: -0.24 (0.28), residues: 315 loop : -0.32 (0.15), residues: 1750 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 535 time to evaluate : 4.820 Fit side-chains outliers start: 129 outliers final: 77 residues processed: 610 average time/residue: 1.6585 time to fit residues: 1223.4834 Evaluate side-chains 601 residues out of total 3905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 524 time to evaluate : 4.676 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 48 residues processed: 29 average time/residue: 0.7004 time to fit residues: 36.0049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 238 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 356 optimal weight: 10.0000 chunk 291 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 429 optimal weight: 7.9990 chunk 463 optimal weight: 10.0000 chunk 382 optimal weight: 5.9990 chunk 425 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 344 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 258 ASN F 386 GLN E 114 ASN G 845 ASN G 901 HIS C 31 ASN M 179 GLN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9184 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.241 38965 Z= 0.760 Angle : 2.167 50.607 52825 Z= 1.423 Chirality : 0.449 6.667 5867 Planarity : 0.005 0.053 6594 Dihedral : 8.238 173.710 5644 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.13 % Favored : 97.81 % Rotamer Outliers : 3.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.12), residues: 4740 helix: 1.32 (0.10), residues: 2676 sheet: -0.15 (0.28), residues: 315 loop : -0.27 (0.15), residues: 1749 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 525 time to evaluate : 6.186 Fit side-chains revert: symmetry clash outliers start: 148 outliers final: 78 residues processed: 618 average time/residue: 1.6622 time to fit residues: 1245.2694 Evaluate side-chains 592 residues out of total 3905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 514 time to evaluate : 4.885 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 53 residues processed: 25 average time/residue: 0.9748 time to fit residues: 39.3505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 424 optimal weight: 4.9990 chunk 322 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 288 optimal weight: 0.6980 chunk 430 optimal weight: 3.9990 chunk 456 optimal weight: 10.0000 chunk 225 optimal weight: 1.9990 chunk 408 optimal weight: 0.0020 chunk 122 optimal weight: 10.0000 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 GLN F 237 GLN F 386 GLN E 114 ASN G 768 ASN G 834 GLN G 845 ASN G 901 HIS M 179 GLN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9149 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.246 38965 Z= 0.717 Angle : 2.153 50.695 52825 Z= 1.419 Chirality : 0.441 6.498 5867 Planarity : 0.004 0.054 6594 Dihedral : 7.825 171.497 5644 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.96 % Favored : 98.00 % Rotamer Outliers : 3.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.12), residues: 4740 helix: 1.57 (0.10), residues: 2676 sheet: -0.12 (0.29), residues: 318 loop : -0.26 (0.15), residues: 1746 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 532 time to evaluate : 4.931 Fit side-chains outliers start: 129 outliers final: 74 residues processed: 616 average time/residue: 1.5810 time to fit residues: 1191.4919 Evaluate side-chains 598 residues out of total 3905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 524 time to evaluate : 4.615 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 53 residues processed: 22 average time/residue: 0.7475 time to fit residues: 30.3268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 379 optimal weight: 6.9990 chunk 258 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 339 optimal weight: 0.4980 chunk 188 optimal weight: 0.7980 chunk 389 optimal weight: 0.9990 chunk 315 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 232 optimal weight: 2.9990 chunk 409 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 GLN F 237 GLN G 845 ASN G 901 HIS H 323 GLN M 179 GLN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 285 ASN N 447 ASN K 5 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9152 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.242 38965 Z= 0.721 Angle : 2.153 50.629 52825 Z= 1.419 Chirality : 0.443 6.507 5867 Planarity : 0.004 0.054 6594 Dihedral : 7.742 171.745 5644 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.17 % Favored : 97.78 % Rotamer Outliers : 3.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.12), residues: 4740 helix: 1.68 (0.10), residues: 2673 sheet: -0.07 (0.29), residues: 318 loop : -0.20 (0.15), residues: 1749 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 538 time to evaluate : 4.275 Fit side-chains outliers start: 122 outliers final: 73 residues processed: 618 average time/residue: 1.5986 time to fit residues: 1200.8538 Evaluate side-chains 599 residues out of total 3905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 526 time to evaluate : 4.684 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 53 residues processed: 20 average time/residue: 0.7428 time to fit residues: 28.2771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 153 optimal weight: 0.2980 chunk 410 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 267 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 456 optimal weight: 6.9990 chunk 379 optimal weight: 6.9990 chunk 211 optimal weight: 10.0000 chunk 37 optimal weight: 0.0470 chunk 151 optimal weight: 2.9990 chunk 239 optimal weight: 9.9990 overall best weight: 2.6684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 GLN F 237 GLN ** G 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 261 GLN H 323 GLN M 179 GLN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9154 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.242 38965 Z= 0.723 Angle : 2.155 50.609 52825 Z= 1.419 Chirality : 0.443 6.514 5867 Planarity : 0.004 0.054 6594 Dihedral : 7.733 171.898 5644 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.00 % Favored : 97.95 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.12), residues: 4740 helix: 1.71 (0.10), residues: 2668 sheet: -0.07 (0.29), residues: 318 loop : -0.17 (0.15), residues: 1754 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 532 time to evaluate : 4.769 Fit side-chains outliers start: 111 outliers final: 69 residues processed: 614 average time/residue: 1.6548 time to fit residues: 1239.0479 Evaluate side-chains 592 residues out of total 3905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 523 time to evaluate : 4.637 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 56 residues processed: 13 average time/residue: 0.7844 time to fit residues: 20.9214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 440 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 260 optimal weight: 10.0000 chunk 333 optimal weight: 2.9990 chunk 258 optimal weight: 9.9990 chunk 384 optimal weight: 6.9990 chunk 255 optimal weight: 0.6980 chunk 454 optimal weight: 10.0000 chunk 284 optimal weight: 0.8980 chunk 277 optimal weight: 5.9990 chunk 210 optimal weight: 9.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 GLN F 237 GLN G 901 HIS H 323 GLN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 GLN K 5 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9127 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.244 38965 Z= 0.713 Angle : 2.150 50.668 52825 Z= 1.417 Chirality : 0.440 6.463 5867 Planarity : 0.004 0.054 6594 Dihedral : 7.459 170.395 5644 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.92 % Favored : 98.06 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.12), residues: 4740 helix: 1.84 (0.10), residues: 2661 sheet: -0.06 (0.29), residues: 326 loop : -0.15 (0.15), residues: 1753 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 539 time to evaluate : 5.137 Fit side-chains outliers start: 101 outliers final: 68 residues processed: 612 average time/residue: 1.6509 time to fit residues: 1239.6911 Evaluate side-chains 597 residues out of total 3905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 529 time to evaluate : 4.795 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 54 residues processed: 14 average time/residue: 0.7304 time to fit residues: 21.2260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 281 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 271 optimal weight: 0.0000 chunk 137 optimal weight: 0.0770 chunk 89 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 289 optimal weight: 2.9990 chunk 309 optimal weight: 10.0000 chunk 224 optimal weight: 9.9990 chunk 42 optimal weight: 50.0000 chunk 357 optimal weight: 9.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 GLN F 237 GLN G 834 GLN H 323 GLN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 GLN N 447 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.244 38965 Z= 0.713 Angle : 2.150 50.645 52825 Z= 1.417 Chirality : 0.440 6.442 5867 Planarity : 0.004 0.053 6594 Dihedral : 7.325 170.245 5644 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.92 % Favored : 98.06 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.12), residues: 4740 helix: 1.89 (0.10), residues: 2661 sheet: -0.18 (0.28), residues: 339 loop : -0.10 (0.15), residues: 1740 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 532 time to evaluate : 5.023 Fit side-chains outliers start: 84 outliers final: 62 residues processed: 595 average time/residue: 1.6588 time to fit residues: 1213.4167 Evaluate side-chains 584 residues out of total 3905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 522 time to evaluate : 4.950 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 54 residues processed: 8 average time/residue: 0.8949 time to fit residues: 16.6338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 413 optimal weight: 6.9990 chunk 435 optimal weight: 5.9990 chunk 397 optimal weight: 0.9990 chunk 423 optimal weight: 9.9990 chunk 255 optimal weight: 0.0970 chunk 184 optimal weight: 6.9990 chunk 332 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 383 optimal weight: 8.9990 chunk 400 optimal weight: 1.9990 chunk 422 optimal weight: 5.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN G 834 GLN ** G 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 GLN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9152 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.243 38965 Z= 0.725 Angle : 2.157 50.621 52825 Z= 1.420 Chirality : 0.443 6.596 5867 Planarity : 0.004 0.054 6594 Dihedral : 7.563 172.174 5644 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.24 % Favored : 97.74 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.12), residues: 4740 helix: 1.80 (0.10), residues: 2663 sheet: -0.09 (0.29), residues: 327 loop : -0.07 (0.15), residues: 1750 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 528 time to evaluate : 4.542 Fit side-chains outliers start: 80 outliers final: 60 residues processed: 595 average time/residue: 1.6742 time to fit residues: 1215.4058 Evaluate side-chains 584 residues out of total 3905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 524 time to evaluate : 4.879 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 54 residues processed: 7 average time/residue: 1.0109 time to fit residues: 15.5922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 278 optimal weight: 9.9990 chunk 448 optimal weight: 9.9990 chunk 273 optimal weight: 4.9990 chunk 212 optimal weight: 0.7980 chunk 311 optimal weight: 7.9990 chunk 470 optimal weight: 6.9990 chunk 432 optimal weight: 9.9990 chunk 374 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 289 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 GLN F 237 GLN G 768 ASN G 834 GLN G 845 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 GLN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9174 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.242 38965 Z= 0.749 Angle : 2.167 50.569 52825 Z= 1.423 Chirality : 0.447 6.645 5867 Planarity : 0.004 0.054 6594 Dihedral : 8.048 173.680 5644 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.22 % Favored : 97.72 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.12), residues: 4740 helix: 1.61 (0.10), residues: 2682 sheet: -0.03 (0.29), residues: 320 loop : -0.11 (0.15), residues: 1738 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 518 time to evaluate : 4.644 Fit side-chains outliers start: 72 outliers final: 58 residues processed: 578 average time/residue: 1.6598 time to fit residues: 1166.2493 Evaluate side-chains 576 residues out of total 3905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 518 time to evaluate : 4.568 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 53 residues processed: 5 average time/residue: 0.7774 time to fit residues: 11.5291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 297 optimal weight: 9.9990 chunk 398 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 345 optimal weight: 0.7980 chunk 55 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 375 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 chunk 385 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 GLN F 237 GLN ** G 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 GLN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 285 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.084163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.066730 restraints weight = 33667.828| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 0.91 r_work: 0.2730 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.242 38965 Z= 0.756 Angle : 2.171 50.564 52825 Z= 1.424 Chirality : 0.448 6.648 5867 Planarity : 0.004 0.054 6594 Dihedral : 8.276 173.508 5644 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.28 % Favored : 97.66 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.12), residues: 4740 helix: 1.57 (0.10), residues: 2675 sheet: -0.05 (0.29), residues: 320 loop : -0.13 (0.15), residues: 1745 =============================================================================== Job complete usr+sys time: 20180.70 seconds wall clock time: 355 minutes 40.58 seconds (21340.58 seconds total)