Starting phenix.real_space_refine on Thu Apr 11 04:06:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sy5_40862/04_2024/8sy5_40862_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sy5_40862/04_2024/8sy5_40862.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sy5_40862/04_2024/8sy5_40862_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sy5_40862/04_2024/8sy5_40862_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sy5_40862/04_2024/8sy5_40862_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sy5_40862/04_2024/8sy5_40862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sy5_40862/04_2024/8sy5_40862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sy5_40862/04_2024/8sy5_40862_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sy5_40862/04_2024/8sy5_40862_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 45 5.49 5 Mg 1 5.21 5 S 93 5.16 5 C 13085 2.51 5 N 3762 2.21 5 O 4423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "G ASP 15": "OD1" <-> "OD2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G ASP 77": "OD1" <-> "OD2" Residue "G ASP 118": "OD1" <-> "OD2" Residue "G GLU 136": "OE1" <-> "OE2" Residue "G ASP 212": "OD1" <-> "OD2" Residue "I ASP 23": "OD1" <-> "OD2" Residue "I TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 126": "OE1" <-> "OE2" Residue "I GLU 142": "OE1" <-> "OE2" Residue "I PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 199": "OD1" <-> "OD2" Residue "I PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 423": "OD1" <-> "OD2" Residue "I GLU 461": "OE1" <-> "OE2" Residue "I ASP 516": "OD1" <-> "OD2" Residue "I ASP 601": "OD1" <-> "OD2" Residue "I ASP 654": "OD1" <-> "OD2" Residue "I GLU 848": "OE1" <-> "OE2" Residue "I GLU 950": "OE1" <-> "OE2" Residue "I TYR 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1084": "OD1" <-> "OD2" Residue "I GLU 1143": "OE1" <-> "OE2" Residue "I ASP 1241": "OD1" <-> "OD2" Residue "I TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 54": "OD1" <-> "OD2" Residue "J ARG 60": "NH1" <-> "NH2" Residue "J ASP 308": "OD1" <-> "OD2" Residue "J GLU 418": "OE1" <-> "OE2" Residue "J ASP 464": "OD1" <-> "OD2" Residue "J TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 811": "OE1" <-> "OE2" Residue "J GLU 913": "OE1" <-> "OE2" Residue "J PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1146": "OE1" <-> "OE2" Residue "J ASP 1305": "OD1" <-> "OD2" Residue "J PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 44": "OD1" <-> "OD2" Residue "K GLU 50": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 21411 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1639 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 41 Chain: "G" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1690 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "I" Number of atoms: 8556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 8556 Classifications: {'peptide': 1136} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 49, 'TRANS': 1086} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 407 Unresolved non-hydrogen angles: 501 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU%COO:plan': 1, 'ASP:plan': 14, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 29, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 254 Chain: "J" Number of atoms: 7684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7684 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 42, 'TRANS': 989} Chain breaks: 6 Unresolved non-hydrogen bonds: 388 Unresolved non-hydrogen angles: 474 Unresolved non-hydrogen dihedrals: 302 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 24, 'ARG:plan': 18, 'ASN:plan1': 2, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 243 Chain: "K" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 528 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "N" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 249 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} Chain: "R" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 194 Classifications: {'RNA': 9} Modifications used: {'5*END': 1, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 461 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "J" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 1, ' ZN': 2, 'X0F': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "I" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "J" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 142 Classifications: {'water': 142} Link IDs: {None: 141} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12323 SG CYS J 70 19.251 44.439 88.349 1.00 55.55 S ATOM 12337 SG CYS J 72 18.077 41.031 87.290 1.00 60.57 S ATOM 12445 SG CYS J 85 17.498 42.370 90.986 1.00 61.61 S ATOM 12469 SG CYS J 88 20.741 41.055 89.746 1.00 63.64 S ATOM 17517 SG CYS J 814 47.184 105.293 103.256 1.00 41.05 S ATOM 17983 SG CYS J 888 48.610 103.350 100.786 1.00 33.55 S ATOM 18034 SG CYS J 895 46.757 105.221 98.740 1.00 24.28 S Time building chain proxies: 11.42, per 1000 atoms: 0.53 Number of scatterers: 21411 At special positions: 0 Unit cell: (125.56, 164.26, 141.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 93 16.00 P 45 15.00 Mg 1 11.99 O 4423 8.00 N 3762 7.00 C 13085 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: 8.44 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " Number of angles added : 6 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4956 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 25 sheets defined 36.7% alpha, 12.8% beta 11 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 9.62 Creating SS restraints... Processing helix chain 'A' and resid 35 through 49 removed outlier: 3.672A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.721A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 213 through 228 removed outlier: 3.718A pdb=" N GLN A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 47 Processing helix chain 'G' and resid 78 through 87 removed outlier: 4.057A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 155 through 158 No H-bonds generated for 'chain 'G' and resid 155 through 158' Processing helix chain 'G' and resid 213 through 231 removed outlier: 3.750A pdb=" N GLU G 229 " --> pdb=" O ALA G 225 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 8 No H-bonds generated for 'chain 'I' and resid 5 through 8' Processing helix chain 'I' and resid 29 through 39 removed outlier: 3.677A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS I 37 " --> pdb=" O ASP I 33 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE I 38 " --> pdb=" O SER I 34 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE I 39 " --> pdb=" O PHE I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 54 Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 346 through 353 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 389 removed outlier: 3.640A pdb=" N PHE I 385 " --> pdb=" O ALA I 381 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 456 through 478 removed outlier: 3.732A pdb=" N GLU I 461 " --> pdb=" O GLY I 457 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL I 471 " --> pdb=" O GLY I 467 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU I 472 " --> pdb=" O LEU I 468 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG I 473 " --> pdb=" O VAL I 469 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 489 through 492 Processing helix chain 'I' and resid 496 through 508 removed outlier: 4.091A pdb=" N GLY I 507 " --> pdb=" O LYS I 503 " (cutoff:3.500A) Processing helix chain 'I' and resid 520 through 528 removed outlier: 3.561A pdb=" N ILE I 524 " --> pdb=" O PRO I 520 " (cutoff:3.500A) Processing helix chain 'I' and resid 552 through 554 No H-bonds generated for 'chain 'I' and resid 552 through 554' Processing helix chain 'I' and resid 610 through 613 Processing helix chain 'I' and resid 647 through 649 No H-bonds generated for 'chain 'I' and resid 647 through 649' Processing helix chain 'I' and resid 665 through 667 No H-bonds generated for 'chain 'I' and resid 665 through 667' Processing helix chain 'I' and resid 671 through 673 No H-bonds generated for 'chain 'I' and resid 671 through 673' Processing helix chain 'I' and resid 676 through 687 removed outlier: 4.220A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 712 Processing helix chain 'I' and resid 738 through 740 No H-bonds generated for 'chain 'I' and resid 738 through 740' Processing helix chain 'I' and resid 820 through 824 Processing helix chain 'I' and resid 860 through 864 removed outlier: 4.317A pdb=" N LYS I 864 " --> pdb=" O ALA I 861 " (cutoff:3.500A) Processing helix chain 'I' and resid 943 through 947 Processing helix chain 'I' and resid 949 through 975 removed outlier: 3.812A pdb=" N LEU I 953 " --> pdb=" O GLU I 949 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE I 966 " --> pdb=" O GLU I 962 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU I 967 " --> pdb=" O GLU I 963 " (cutoff:3.500A) Processing helix chain 'I' and resid 1018 through 1036 Processing helix chain 'I' and resid 1082 through 1084 No H-bonds generated for 'chain 'I' and resid 1082 through 1084' Processing helix chain 'I' and resid 1100 through 1102 No H-bonds generated for 'chain 'I' and resid 1100 through 1102' Processing helix chain 'I' and resid 1109 through 1133 removed outlier: 4.023A pdb=" N GLU I1114 " --> pdb=" O GLN I1111 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY I1118 " --> pdb=" O THR I1115 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET I1119 " --> pdb=" O HIS I1116 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS I1122 " --> pdb=" O MET I1119 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP I1126 " --> pdb=" O GLY I1123 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA I1130 " --> pdb=" O LYS I1127 " (cutoff:3.500A) Processing helix chain 'I' and resid 1138 through 1149 Processing helix chain 'I' and resid 1161 through 1163 No H-bonds generated for 'chain 'I' and resid 1161 through 1163' Processing helix chain 'I' and resid 1166 through 1175 Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 1241 No H-bonds generated for 'chain 'I' and resid 1239 through 1241' Processing helix chain 'I' and resid 1272 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1298 through 1310 removed outlier: 3.784A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1321 through 1333 removed outlier: 3.708A pdb=" N LEU I1333 " --> pdb=" O GLU I1329 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 59 through 62 No H-bonds generated for 'chain 'J' and resid 59 through 62' Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 95 through 99 Processing helix chain 'J' and resid 114 through 117 No H-bonds generated for 'chain 'J' and resid 114 through 117' Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 182 through 190 Processing helix chain 'J' and resid 194 through 204 Processing helix chain 'J' and resid 217 through 230 Processing helix chain 'J' and resid 234 through 237 removed outlier: 3.873A pdb=" N MET J 237 " --> pdb=" O PRO J 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 234 through 237' Processing helix chain 'J' and resid 247 through 249 No H-bonds generated for 'chain 'J' and resid 247 through 249' Processing helix chain 'J' and resid 265 through 285 removed outlier: 3.658A pdb=" N LEU J 282 " --> pdb=" O ARG J 278 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU J 283 " --> pdb=" O LEU J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 307 removed outlier: 3.607A pdb=" N ASN J 294 " --> pdb=" O ILE J 290 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG J 297 " --> pdb=" O ARG J 293 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN J 300 " --> pdb=" O LYS J 296 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA J 305 " --> pdb=" O GLU J 301 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 330 Processing helix chain 'J' and resid 337 through 341 Processing helix chain 'J' and resid 370 through 376 removed outlier: 3.713A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 378 through 387 Processing helix chain 'J' and resid 394 through 403 removed outlier: 4.009A pdb=" N LYS J 398 " --> pdb=" O ILE J 394 " (cutoff:3.500A) Processing helix chain 'J' and resid 408 through 416 removed outlier: 3.785A pdb=" N ASP J 413 " --> pdb=" O TRP J 409 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE J 416 " --> pdb=" O LEU J 412 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 433 No H-bonds generated for 'chain 'J' and resid 431 through 433' Processing helix chain 'J' and resid 451 through 457 removed outlier: 3.760A pdb=" N CYS J 454 " --> pdb=" O PRO J 451 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ALA J 455 " --> pdb=" O LEU J 452 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA J 456 " --> pdb=" O VAL J 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 482 Processing helix chain 'J' and resid 505 through 514 Processing helix chain 'J' and resid 530 through 539 Processing helix chain 'J' and resid 574 through 582 removed outlier: 4.190A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ILE J 582 " --> pdb=" O ILE J 578 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 591 No H-bonds generated for 'chain 'J' and resid 589 through 591' Processing helix chain 'J' and resid 598 through 611 Processing helix chain 'J' and resid 615 through 635 removed outlier: 3.849A pdb=" N ILE J 619 " --> pdb=" O LYS J 615 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA J 633 " --> pdb=" O PHE J 629 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG J 634 " --> pdb=" O ALA J 630 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER J 635 " --> pdb=" O TYR J 631 " (cutoff:3.500A) Processing helix chain 'J' and resid 641 through 643 No H-bonds generated for 'chain 'J' and resid 641 through 643' Processing helix chain 'J' and resid 650 through 669 removed outlier: 3.603A pdb=" N GLN J 665 " --> pdb=" O VAL J 661 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU J 666 " --> pdb=" O ALA J 662 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN J 667 " --> pdb=" O GLU J 663 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE J 668 " --> pdb=" O ILE J 664 " (cutoff:3.500A) Processing helix chain 'J' and resid 678 through 702 Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 734 through 741 removed outlier: 3.680A pdb=" N ARG J 738 " --> pdb=" O ALA J 734 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN J 739 " --> pdb=" O ALA J 735 " (cutoff:3.500A) Processing helix chain 'J' and resid 769 through 788 removed outlier: 3.635A pdb=" N THR J 776 " --> pdb=" O TYR J 772 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) Processing helix chain 'J' and resid 790 through 803 Processing helix chain 'J' and resid 836 through 839 No H-bonds generated for 'chain 'J' and resid 836 through 839' Processing helix chain 'J' and resid 866 through 874 Processing helix chain 'J' and resid 896 through 899 No H-bonds generated for 'chain 'J' and resid 896 through 899' Processing helix chain 'J' and resid 915 through 931 Proline residue: J 926 - end of helix Processing helix chain 'J' and resid 934 through 936 No H-bonds generated for 'chain 'J' and resid 934 through 936' Processing helix chain 'J' and resid 1138 through 1144 Processing helix chain 'J' and resid 1217 through 1224 Processing helix chain 'J' and resid 1226 through 1243 removed outlier: 3.784A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU J1243 " --> pdb=" O ASP J1239 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1260 Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.654A pdb=" N ASN J1295 " --> pdb=" O GLU J1291 " (cutoff:3.500A) Processing helix chain 'J' and resid 1309 through 1314 removed outlier: 3.549A pdb=" N LEU J1314 " --> pdb=" O THR J1310 " (cutoff:3.500A) Processing helix chain 'J' and resid 1319 through 1325 Processing helix chain 'J' and resid 1328 through 1338 Processing helix chain 'J' and resid 1347 through 1353 Processing helix chain 'J' and resid 1360 through 1372 removed outlier: 4.679A pdb=" N ALA J1364 " --> pdb=" O THR J1361 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET J1370 " --> pdb=" O GLN J1367 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 21 removed outlier: 3.555A pdb=" N GLU K 19 " --> pdb=" O GLN K 15 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS K 20 " --> pdb=" O ASP K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 39 removed outlier: 3.629A pdb=" N VAL K 28 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU K 29 " --> pdb=" O PHE K 25 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN K 37 " --> pdb=" O ARG K 33 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET K 38 " --> pdb=" O ARG K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 64 Processing helix chain 'K' and resid 69 through 79 Processing sheet with id= A, first strand: chain 'A' and resid 13 through 20 removed outlier: 6.561A pdb=" N HIS A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.788A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 108 through 111 Processing sheet with id= E, first strand: chain 'G' and resid 12 through 18 removed outlier: 6.750A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLN G 18 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N HIS G 23 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 170 through 172 removed outlier: 6.882A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 90 through 92 Processing sheet with id= H, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.511A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= J, first strand: chain 'I' and resid 148 through 151 Processing sheet with id= K, first strand: chain 'I' and resid 154 through 160 removed outlier: 4.177A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 529 through 531 Processing sheet with id= M, first strand: chain 'I' and resid 588 through 592 Processing sheet with id= N, first strand: chain 'I' and resid 634 through 638 Processing sheet with id= O, first strand: chain 'I' and resid 748 through 752 removed outlier: 3.808A pdb=" N ARG I 731 " --> pdb=" O ASP I 728 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR I 726 " --> pdb=" O VAL I 733 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 1226 through 1232 removed outlier: 4.571A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 1065 through 1067 removed outlier: 7.595A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 69 through 75 removed outlier: 6.782A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY I 125 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL I 98 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N TYR I 123 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU I 100 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU I 121 " --> pdb=" O LEU I 100 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.768A pdb=" N SER I 840 " --> pdb=" O LYS I1048 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 103 through 106 Processing sheet with id= U, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= V, first strand: chain 'J' and resid 355 through 357 removed outlier: 6.037A pdb=" N ILE J 447 " --> pdb=" O THR J 356 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'J' and resid 547 through 557 Processing sheet with id= X, first strand: chain 'J' and resid 707 through 709 Processing sheet with id= Y, first strand: chain 'J' and resid 820 through 822 removed outlier: 3.674A pdb=" N VAL J 880 " --> pdb=" O MET J 822 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 1938 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 9.98 Time building geometry restraints manager: 9.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3513 1.31 - 1.43: 5380 1.43 - 1.56: 12302 1.56 - 1.69: 91 1.69 - 1.81: 159 Bond restraints: 21445 Sorted by residual: bond pdb=" C23 X0F J1504 " pdb=" N24 X0F J1504 " ideal model delta sigma weight residual 0.000 1.450 -1.450 2.00e-02 2.50e+03 5.26e+03 bond pdb=" C22 X0F J1504 " pdb=" C29 X0F J1504 " ideal model delta sigma weight residual 2.611 1.357 1.254 2.00e-02 2.50e+03 3.93e+03 bond pdb=" C20 X0F J1504 " pdb=" N21 X0F J1504 " ideal model delta sigma weight residual 2.162 1.347 0.815 2.00e-02 2.50e+03 1.66e+03 bond pdb=" C26 X0F J1504 " pdb=" N25 X0F J1504 " ideal model delta sigma weight residual 2.208 1.441 0.767 2.00e-02 2.50e+03 1.47e+03 bond pdb=" C26 X0F J1504 " pdb=" N28 X0F J1504 " ideal model delta sigma weight residual 0.954 1.462 -0.508 2.00e-02 2.50e+03 6.44e+02 ... (remaining 21440 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.60: 801 106.60 - 113.84: 12196 113.84 - 121.07: 10079 121.07 - 128.31: 6045 128.31 - 135.55: 136 Bond angle restraints: 29257 Sorted by residual: angle pdb=" N24 X0F J1504 " pdb=" C23 X0F J1504 " pdb=" N25 X0F J1504 " ideal model delta sigma weight residual 59.24 119.67 -60.43 3.00e+00 1.11e-01 4.06e+02 angle pdb=" C23 X0F J1504 " pdb=" C22 X0F J1504 " pdb=" N21 X0F J1504 " ideal model delta sigma weight residual 175.74 131.77 43.97 3.00e+00 1.11e-01 2.15e+02 angle pdb=" C23 X0F J1504 " pdb=" C22 X0F J1504 " pdb=" C29 X0F J1504 " ideal model delta sigma weight residual 76.41 120.19 -43.78 3.00e+00 1.11e-01 2.13e+02 angle pdb=" C22 X0F J1504 " pdb=" C23 X0F J1504 " pdb=" N25 X0F J1504 " ideal model delta sigma weight residual 152.80 120.15 32.65 3.00e+00 1.11e-01 1.18e+02 angle pdb=" C22 X0F J1504 " pdb=" C23 X0F J1504 " pdb=" N24 X0F J1504 " ideal model delta sigma weight residual 93.55 120.18 -26.63 3.00e+00 1.11e-01 7.88e+01 ... (remaining 29252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.74: 12196 27.74 - 55.47: 657 55.47 - 83.21: 76 83.21 - 110.95: 11 110.95 - 138.68: 1 Dihedral angle restraints: 12941 sinusoidal: 5248 harmonic: 7693 Sorted by residual: dihedral pdb=" CA GLU J 42 " pdb=" C GLU J 42 " pdb=" N THR J 43 " pdb=" CA THR J 43 " ideal model delta harmonic sigma weight residual 180.00 -151.99 -28.01 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA GLY A 119 " pdb=" C GLY A 119 " pdb=" N ASP A 120 " pdb=" CA ASP A 120 " ideal model delta harmonic sigma weight residual -180.00 -154.78 -25.22 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ARG J 425 " pdb=" C ARG J 425 " pdb=" N ALA J 426 " pdb=" CA ALA J 426 " ideal model delta harmonic sigma weight residual -180.00 -155.32 -24.68 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 12938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3111 0.077 - 0.153: 300 0.153 - 0.230: 2 0.230 - 0.307: 1 0.307 - 0.383: 1 Chirality restraints: 3415 Sorted by residual: chirality pdb=" C16 X0F J1504 " pdb=" C15 X0F J1504 " pdb=" C17 X0F J1504 " pdb=" O32 X0F J1504 " both_signs ideal model delta sigma weight residual False 2.23 2.61 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" C3' JSP T 19 " pdb=" C4' JSP T 19 " pdb=" O3' JSP T 19 " pdb=" C2' JSP T 19 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C17 X0F J1504 " pdb=" C16 X0F J1504 " pdb=" C18 X0F J1504 " pdb=" O31 X0F J1504 " both_signs ideal model delta sigma weight residual False 2.56 2.40 0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 3412 not shown) Planarity restraints: 3664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 119 " -0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C GLY A 119 " 0.060 2.00e-02 2.50e+03 pdb=" O GLY A 119 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP A 120 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN I 519 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO I 520 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO I 520 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO I 520 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 40 " -0.035 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO J 41 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO J 41 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO J 41 " -0.029 5.00e-02 4.00e+02 ... (remaining 3661 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.13: 4 2.13 - 2.82: 5831 2.82 - 3.51: 26113 3.51 - 4.21: 46819 4.21 - 4.90: 84461 Nonbonded interactions: 163228 Sorted by model distance: nonbonded pdb=" OD1 ASP J 460 " pdb=" OD2 ASP J 464 " model vdw 1.432 3.040 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1503 " model vdw 1.959 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1503 " model vdw 2.045 2.170 nonbonded pdb=" OD2 ASP J 460 " pdb=" OD2 ASP J 462 " model vdw 2.124 3.040 nonbonded pdb=" OD2 ASP J 464 " pdb="MG MG J1503 " model vdw 2.174 2.170 ... (remaining 163223 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 187 or (resid 188 through 194 and (name N or nam \ e CA or name C or name O or name CB )) or resid 195 through 196 or (resid 197 an \ d (name N or name CA or name C or name O or name CB )) or resid 198 through 233) \ ) selection = (chain 'G' and (resid 6 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 19 or (resid 20 and (name N or name \ CA or name C or name O or name CB )) or resid 21 through 64 or (resid 65 and (n \ ame N or name CA or name C or name O or name CB )) or resid 66 through 70 or (re \ sid 71 through 72 and (name N or name CA or name C or name O or name CB )) or re \ sid 73 through 74 or (resid 75 and (name N or name CA or name C or name O or nam \ e CB )) or resid 76 or (resid 77 and (name N or name CA or name C or name O or n \ ame CB )) or resid 78 through 94 or (resid 95 through 96 and (name N or name CA \ or name C or name O or name CB )) or resid 97 through 106 or (resid 107 and (nam \ e N or name CA or name C or name O or name CB )) or resid 108 through 117 or (re \ sid 118 and (name N or name CA or name C or name O or name CB )) or resid 119 th \ rough 133 or (resid 134 through 135 and (name N or name CA or name C or name O o \ r name CB )) or resid 136 or (resid 137 through 138 and (name N or name CA or na \ me C or name O or name CB )) or resid 139 through 158 or (resid 159 and (name N \ or name CA or name C or name O or name CB )) or (resid 168 and (name N or name C \ A or name C or name O or name CB )) or resid 169 or (resid 170 and (name N or na \ me CA or name C or name O or name CB )) or resid 171 through 233)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 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: 7.870 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 66.550 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.090 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:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 : 0.017 1.450 21445 Z= 0.760 Angle : 0.808 60.428 29257 Z= 0.360 Chirality : 0.043 0.383 3415 Planarity : 0.005 0.054 3664 Dihedral : 16.067 138.684 7985 Min Nonbonded Distance : 1.432 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % 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: 0.01 (0.16), residues: 2646 helix: 1.26 (0.17), residues: 954 sheet: 0.61 (0.29), residues: 319 loop : -1.07 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 580 HIS 0.008 0.001 HIS A 23 PHE 0.015 0.001 PHE I 514 TYR 0.014 0.001 TYR J 269 ARG 0.007 0.000 ARG J1148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 2.336 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 1.6892 time to fit residues: 470.0396 Evaluate side-chains 168 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 0.5980 chunk 204 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN G 147 GLN G 186 ASN K 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21445 Z= 0.248 Angle : 0.558 10.602 29257 Z= 0.293 Chirality : 0.042 0.165 3415 Planarity : 0.005 0.074 3664 Dihedral : 12.048 139.673 3415 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.67 % Favored : 96.30 % Rotamer: Outliers : 0.74 % Allowed : 6.89 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2646 helix: 1.49 (0.17), residues: 956 sheet: 0.43 (0.28), residues: 337 loop : -1.04 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 580 HIS 0.009 0.001 HIS A 66 PHE 0.011 0.001 PHE I 514 TYR 0.013 0.001 TYR I 367 ARG 0.011 0.000 ARG J 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 175 time to evaluate : 2.679 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.6721 (OUTLIER) cc_final: 0.6354 (p0) outliers start: 15 outliers final: 5 residues processed: 183 average time/residue: 1.7106 time to fit residues: 354.6553 Evaluate side-chains 169 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 163 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 788 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 245 optimal weight: 3.9990 chunk 265 optimal weight: 0.0010 chunk 218 optimal weight: 0.0270 chunk 243 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 overall best weight: 1.8050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21445 Z= 0.248 Angle : 0.558 10.600 29257 Z= 0.293 Chirality : 0.042 0.165 3415 Planarity : 0.005 0.074 3664 Dihedral : 12.048 139.673 3415 Min Nonbonded Distance : 1.520 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.67 % Favored : 96.30 % Rotamer: Outliers : 0.30 % Allowed : 8.71 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2646 helix: 1.49 (0.17), residues: 956 sheet: 0.43 (0.28), residues: 337 loop : -1.04 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 580 HIS 0.009 0.001 HIS A 66 PHE 0.011 0.001 PHE I 514 TYR 0.013 0.001 TYR I 367 ARG 0.011 0.000 ARG J 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 163 time to evaluate : 2.515 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.6722 (OUTLIER) cc_final: 0.6354 (p0) outliers start: 6 outliers final: 5 residues processed: 167 average time/residue: 1.5751 time to fit residues: 297.2840 Evaluate side-chains 169 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 163 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 788 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 7.9990 chunk 184 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 246 optimal weight: 9.9990 chunk 260 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21445 Z= 0.248 Angle : 0.559 10.598 29257 Z= 0.293 Chirality : 0.042 0.165 3415 Planarity : 0.005 0.074 3664 Dihedral : 12.048 139.674 3415 Min Nonbonded Distance : 1.523 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.67 % Favored : 96.30 % Rotamer: Outliers : 0.30 % Allowed : 8.71 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2646 helix: 1.49 (0.17), residues: 956 sheet: 0.43 (0.28), residues: 337 loop : -1.04 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 580 HIS 0.009 0.001 HIS A 66 PHE 0.011 0.001 PHE I 514 TYR 0.013 0.001 TYR I 367 ARG 0.011 0.000 ARG J 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 163 time to evaluate : 2.744 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.6722 (OUTLIER) cc_final: 0.6354 (p0) outliers start: 6 outliers final: 5 residues processed: 167 average time/residue: 1.5786 time to fit residues: 298.1793 Evaluate side-chains 169 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 163 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 788 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 20.0000 chunk 148 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 222 optimal weight: 9.9990 chunk 180 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 133 optimal weight: 0.2980 chunk 234 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21445 Z= 0.247 Angle : 0.562 10.581 29257 Z= 0.293 Chirality : 0.042 0.166 3415 Planarity : 0.005 0.073 3664 Dihedral : 12.048 139.675 3415 Min Nonbonded Distance : 1.557 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.39 % Allowed : 8.61 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2646 helix: 1.49 (0.17), residues: 956 sheet: 0.43 (0.28), residues: 337 loop : -1.04 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 580 HIS 0.008 0.001 HIS J 817 PHE 0.011 0.001 PHE I 514 TYR 0.013 0.001 TYR I 367 ARG 0.011 0.000 ARG J 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 163 time to evaluate : 2.506 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.6722 (OUTLIER) cc_final: 0.6354 (p0) outliers start: 8 outliers final: 6 residues processed: 167 average time/residue: 1.5637 time to fit residues: 295.7347 Evaluate side-chains 170 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 163 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 788 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 3.9990 chunk 235 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 chunk 120 optimal weight: 0.3980 chunk 21 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21445 Z= 0.250 Angle : 0.560 10.558 29257 Z= 0.293 Chirality : 0.042 0.166 3415 Planarity : 0.005 0.073 3664 Dihedral : 12.048 139.677 3415 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.34 % Allowed : 8.71 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2646 helix: 1.49 (0.17), residues: 956 sheet: 0.43 (0.28), residues: 337 loop : -1.04 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 580 HIS 0.008 0.001 HIS J 817 PHE 0.011 0.001 PHE I 514 TYR 0.012 0.001 TYR J 68 ARG 0.010 0.000 ARG J 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 163 time to evaluate : 2.409 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.6722 (OUTLIER) cc_final: 0.6354 (p0) outliers start: 7 outliers final: 6 residues processed: 167 average time/residue: 1.5537 time to fit residues: 293.2697 Evaluate side-chains 170 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 163 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 788 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 145 optimal weight: 0.4980 chunk 260 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21445 Z= 0.247 Angle : 0.550 10.741 29257 Z= 0.287 Chirality : 0.042 0.238 3415 Planarity : 0.005 0.100 3664 Dihedral : 12.093 141.998 3415 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.79 % Allowed : 8.22 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % 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: 0.19 (0.16), residues: 2646 helix: 1.54 (0.17), residues: 959 sheet: 0.41 (0.28), residues: 337 loop : -1.02 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 183 HIS 0.005 0.001 HIS A 23 PHE 0.012 0.001 PHE J1325 TYR 0.020 0.001 TYR I 5 ARG 0.019 0.000 ARG I 378 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 2.600 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.6755 (OUTLIER) cc_final: 0.6334 (p0) outliers start: 16 outliers final: 9 residues processed: 171 average time/residue: 1.5079 time to fit residues: 292.9653 Evaluate side-chains 167 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 157 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 788 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN K 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 21445 Z= 0.214 Angle : 0.547 10.869 29257 Z= 0.286 Chirality : 0.042 0.301 3415 Planarity : 0.005 0.115 3664 Dihedral : 12.083 142.391 3415 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.74 % Allowed : 8.46 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % 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: 0.22 (0.16), residues: 2646 helix: 1.55 (0.17), residues: 958 sheet: 0.42 (0.28), residues: 342 loop : -0.99 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 183 HIS 0.005 0.001 HIS A 66 PHE 0.011 0.001 PHE J1325 TYR 0.012 0.001 TYR I 5 ARG 0.017 0.000 ARG I 378 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 163 time to evaluate : 2.534 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 169 average time/residue: 1.5622 time to fit residues: 299.5835 Evaluate side-chains 168 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 161 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 788 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 8.9990 chunk 249 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 242 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 chunk 190 optimal weight: 0.1980 chunk 74 optimal weight: 0.0010 chunk 219 optimal weight: 0.9990 chunk 229 optimal weight: 6.9990 chunk 241 optimal weight: 4.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 21445 Z= 0.158 Angle : 0.535 11.763 29257 Z= 0.279 Chirality : 0.041 0.262 3415 Planarity : 0.005 0.130 3664 Dihedral : 12.067 142.176 3415 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.54 % Allowed : 8.86 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2646 helix: 1.64 (0.17), residues: 958 sheet: 0.47 (0.28), residues: 342 loop : -0.95 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 183 HIS 0.006 0.001 HIS A 66 PHE 0.011 0.001 PHE I 514 TYR 0.021 0.001 TYR I 3 ARG 0.022 0.000 ARG I 378 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 168 time to evaluate : 2.326 Fit side-chains revert: symmetry clash REVERT: A 205 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6623 (ttp) outliers start: 11 outliers final: 7 residues processed: 171 average time/residue: 1.5799 time to fit residues: 305.7128 Evaluate side-chains 169 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 161 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 788 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 4.9990 chunk 256 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 178 optimal weight: 0.9990 chunk 268 optimal weight: 10.0000 chunk 247 optimal weight: 4.9990 chunk 214 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 165 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 21445 Z= 0.158 Angle : 0.536 11.753 29257 Z= 0.279 Chirality : 0.041 0.261 3415 Planarity : 0.005 0.130 3664 Dihedral : 12.067 142.176 3415 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.39 % Allowed : 9.35 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2646 helix: 1.64 (0.17), residues: 958 sheet: 0.47 (0.28), residues: 342 loop : -0.95 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 183 HIS 0.006 0.001 HIS A 66 PHE 0.011 0.001 PHE I 514 TYR 0.022 0.001 TYR I 3 ARG 0.022 0.000 ARG I 378 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 162 time to evaluate : 2.544 Fit side-chains revert: symmetry clash REVERT: A 205 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6623 (ttp) outliers start: 8 outliers final: 7 residues processed: 165 average time/residue: 1.5498 time to fit residues: 288.9518 Evaluate side-chains 169 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 161 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 788 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 197 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 214 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.095178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.062742 restraints weight = 46311.024| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.27 r_work: 0.2647 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 21445 Z= 0.158 Angle : 0.535 11.753 29257 Z= 0.279 Chirality : 0.041 0.261 3415 Planarity : 0.005 0.130 3664 Dihedral : 12.067 142.176 3415 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.39 % Allowed : 9.35 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2646 helix: 1.64 (0.17), residues: 958 sheet: 0.47 (0.28), residues: 342 loop : -0.95 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 183 HIS 0.006 0.001 HIS A 66 PHE 0.011 0.001 PHE I 514 TYR 0.022 0.001 TYR I 3 ARG 0.022 0.000 ARG I 378 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6381.36 seconds wall clock time: 115 minutes 24.94 seconds (6924.94 seconds total)