Starting phenix.real_space_refine on Wed Feb 21 21:36:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkj_23897/02_2024/7mkj_23897_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkj_23897/02_2024/7mkj_23897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkj_23897/02_2024/7mkj_23897.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkj_23897/02_2024/7mkj_23897.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkj_23897/02_2024/7mkj_23897_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkj_23897/02_2024/7mkj_23897_updated.pdb" } resolution = 2.9 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= 0.003 sd= 0.127 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 118 5.49 5 Mg 1 5.21 5 S 130 5.16 5 C 19726 2.51 5 N 5655 2.21 5 O 6375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ASP 96": "OD1" <-> "OD2" Residue "G ASP 114": "OD1" <-> "OD2" Residue "G GLU 136": "OE1" <-> "OE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "H ASP 62": "OD1" <-> "OD2" Residue "H GLU 67": "OE1" <-> "OE2" Residue "H TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "H ASP 197": "OD1" <-> "OD2" Residue "H GLU 214": "OE1" <-> "OE2" Residue "I PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 222": "OD1" <-> "OD2" Residue "I ARG 268": "NH1" <-> "NH2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 358": "OD1" <-> "OD2" Residue "I GLU 365": "OE1" <-> "OE2" Residue "I PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 392": "OE1" <-> "OE2" Residue "I ASP 393": "OD1" <-> "OD2" Residue "I GLU 412": "OE1" <-> "OE2" Residue "I GLU 477": "OE1" <-> "OE2" Residue "I GLU 583": "OE1" <-> "OE2" Residue "I PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 641": "OE1" <-> "OE2" Residue "I PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 859": "OE1" <-> "OE2" Residue "I GLU 876": "OE1" <-> "OE2" Residue "I ASP 930": "OD1" <-> "OD2" Residue "I ASP 937": "OD1" <-> "OD2" Residue "I GLU 950": "OE1" <-> "OE2" Residue "I TYR 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1143": "OE1" <-> "OE2" Residue "I ARG 1147": "NH1" <-> "NH2" Residue "J PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "J ASP 413": "OD1" <-> "OD2" Residue "J ASP 505": "OD1" <-> "OD2" Residue "J TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 556": "OE1" <-> "OE2" Residue "J GLU 652": "OE1" <-> "OE2" Residue "J PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 684": "OD1" <-> "OD2" Residue "J GLU 846": "OE1" <-> "OE2" Residue "J GLU 874": "OE1" <-> "OE2" Residue "J PHE 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 913": "OE1" <-> "OE2" Residue "J GLU 1327": "OE1" <-> "OE2" Residue "J GLU 1334": "OE1" <-> "OE2" Residue "K GLU 11": "OE1" <-> "OE2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K GLU 41": "OE1" <-> "OE2" Residue "K GLU 42": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "L PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 369": "OE1" <-> "OE2" Residue "L TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 477": "OE1" <-> "OE2" Residue "L GLU 538": "OE1" <-> "OE2" Residue "L PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32007 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1808 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1710 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1281} Chain: "J" Number of atoms: 10386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10386 Classifications: {'peptide': 1336} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3835 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 455} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1278 Classifications: {'DNA': 62} Link IDs: {'rna3p': 61} Chain: "Q" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1140 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain breaks: 1 Chain: "R" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14534 SG CYS J 70 49.377 125.817 73.852 1.00 66.30 S ATOM 14548 SG CYS J 72 52.392 127.808 72.074 1.00 69.18 S ATOM 14656 SG CYS J 85 48.312 126.204 73.071 1.00 77.60 S ATOM 20368 SG CYS J 814 21.527 74.188 106.018 1.00 55.32 S ATOM 20933 SG CYS J 888 25.051 74.948 105.131 1.00 49.66 S ATOM 21005 SG CYS J 898 24.199 73.207 108.089 1.00 41.44 S Time building chain proxies: 17.48, per 1000 atoms: 0.55 Number of scatterers: 32007 At special positions: 0 Unit cell: (151.58, 193.98, 192.92, 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 130 16.00 P 118 15.00 Mg 1 11.99 O 6375 8.00 N 5655 7.00 C 19726 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.15 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6970 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 32 sheets defined 35.7% alpha, 9.4% beta 48 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 15.78 Creating SS restraints... Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 78 through 87 removed outlier: 3.986A 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 230 removed outlier: 4.524A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 49 Processing helix chain 'H' and resid 78 through 86 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 213 through 227 removed outlier: 3.543A pdb=" N GLN H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 38 removed outlier: 4.483A pdb=" N ILE I 30 " --> pdb=" O LEU I 27 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN I 31 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU I 32 " --> pdb=" O SER I 29 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASP I 33 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER I 34 " --> pdb=" O GLN I 31 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE I 35 " --> pdb=" O LEU I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 207 through 212 Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 246 Processing helix chain 'I' and resid 271 through 280 Processing helix chain 'I' and resid 289 through 292 removed outlier: 3.876A pdb=" N ILE I 292 " --> pdb=" O VAL I 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 289 through 292' Processing helix chain 'I' and resid 319 through 326 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: 4.100A 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 479 removed outlier: 3.852A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 507 Processing helix chain 'I' and resid 520 through 527 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 No H-bonds generated for 'chain 'I' and resid 610 through 613' 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 685 Processing helix chain 'I' and resid 705 through 711 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 821 through 824 No H-bonds generated for 'chain 'I' and resid 821 through 824' Processing helix chain 'I' and resid 861 through 863 No H-bonds generated for 'chain 'I' and resid 861 through 863' Processing helix chain 'I' and resid 897 through 906 Processing helix chain 'I' and resid 943 through 980 removed outlier: 4.088A pdb=" N ILE I 966 " --> pdb=" O GLU I 962 " (cutoff:3.500A) Processing helix chain 'I' and resid 994 through 998 removed outlier: 3.923A pdb=" N LEU I 998 " --> pdb=" O ASP I 995 " (cutoff:3.500A) Processing helix chain 'I' and resid 1006 through 1037 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 1104 Proline residue: I1104 - end of helix Processing helix chain 'I' and resid 1110 through 1133 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 1168 through 1175 Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1272 through 1280 Processing helix chain 'I' and resid 1284 through 1291 Processing helix chain 'I' and resid 1298 through 1309 removed outlier: 3.845A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1321 through 1331 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 removed outlier: 3.667A pdb=" N ARG J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 118 No H-bonds generated for 'chain 'J' and resid 115 through 118' Processing helix chain 'J' and resid 123 through 127 Processing helix chain 'J' and resid 132 through 139 removed outlier: 3.641A pdb=" N ARG J 137 " --> pdb=" O ARG J 133 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL J 138 " --> pdb=" O ASP J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 171 Processing helix chain 'J' and resid 182 through 190 Processing helix chain 'J' and resid 194 through 207 removed outlier: 3.809A pdb=" N ASN J 206 " --> pdb=" O ARG J 202 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU J 207 " --> pdb=" O GLU J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 229 Processing helix 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 264 through 284 Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 328 through 330 No H-bonds generated for 'chain 'J' and resid 328 through 330' Processing helix chain 'J' and resid 337 through 341 Processing helix chain 'J' and resid 370 through 376 removed outlier: 3.757A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 378 through 385 removed outlier: 3.524A pdb=" N LYS J 384 " --> pdb=" O PHE J 380 " (cutoff:3.500A) Processing helix chain 'J' and resid 394 through 400 Processing helix chain 'J' and resid 408 through 415 removed outlier: 3.729A pdb=" N GLU J 414 " --> pdb=" O ASP J 410 " (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: 4.308A pdb=" N ALA J 455 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 476 through 482 removed outlier: 3.596A pdb=" N ARG J 481 " --> pdb=" O GLN J 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 506 through 513 Processing helix chain 'J' and resid 530 through 538 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.823A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (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 599 through 609 removed outlier: 3.683A pdb=" N CYS J 608 " --> pdb=" O MET J 604 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 635 removed outlier: 3.565A pdb=" N ASP J 622 " --> pdb=" O VAL J 618 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET J 625 " --> pdb=" O ALA J 621 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR J 631 " --> pdb=" O THR J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 650 through 658 Processing helix chain 'J' and resid 664 through 669 Processing helix chain 'J' and resid 675 through 701 removed outlier: 4.074A pdb=" N ASN J 680 " --> pdb=" O GLY J 676 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP J 684 " --> pdb=" O ASN J 680 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE J 685 " --> pdb=" O LYS J 681 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA J 688 " --> pdb=" O ASP J 684 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP J 691 " --> pdb=" O ALA J 687 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG J 692 " --> pdb=" O ALA J 688 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS J 695 " --> pdb=" O ASP J 691 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET J 698 " --> pdb=" O SER J 694 " (cutoff:3.500A) Processing helix chain 'J' and resid 721 through 727 removed outlier: 3.696A pdb=" N MET J 725 " --> pdb=" O SER J 721 " (cutoff:3.500A) Processing helix chain 'J' and resid 769 through 785 removed outlier: 3.636A pdb=" N ILE J 774 " --> pdb=" O LEU J 770 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER J 775 " --> pdb=" O GLN J 771 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR J 776 " --> pdb=" O TYR J 772 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY J 782 " --> pdb=" O GLY J 778 " (cutoff:3.500A) Processing helix chain 'J' and resid 789 through 804 removed outlier: 3.739A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG J 798 " --> pdb=" O GLY J 794 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA J 804 " --> pdb=" O LEU J 800 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 839 Processing helix chain 'J' and resid 868 through 874 removed outlier: 3.532A pdb=" N LEU J 872 " --> pdb=" O TRP J 868 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU J 873 " --> pdb=" O CYS J 869 " (cutoff:3.500A) Processing helix chain 'J' and resid 885 through 887 No H-bonds generated for 'chain 'J' and resid 885 through 887' Processing helix chain 'J' and resid 915 through 928 removed outlier: 3.654A pdb=" N ALA J 920 " --> pdb=" O GLY J 916 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE J 923 " --> pdb=" O ALA J 919 " (cutoff:3.500A) Proline residue: J 926 - end of helix Processing helix chain 'J' and resid 1069 through 1072 No H-bonds generated for 'chain 'J' and resid 1069 through 1072' Processing helix chain 'J' and resid 1138 through 1145 Processing helix chain 'J' and resid 1217 through 1224 Processing helix chain 'J' and resid 1226 through 1236 Processing helix chain 'J' and resid 1238 through 1244 removed outlier: 3.825A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1251 through 1258 removed outlier: 3.856A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1294 removed outlier: 3.861A pdb=" N ASN J1289 " --> pdb=" O VAL J1285 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG J1290 " --> pdb=" O LYS J1286 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU J1291 " --> pdb=" O ILE J1287 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU J1292 " --> pdb=" O ALA J1288 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU J1293 " --> pdb=" O ASN J1289 " (cutoff:3.500A) Processing helix chain 'J' and resid 1320 through 1323 No H-bonds generated for 'chain 'J' and resid 1320 through 1323' Processing helix chain 'J' and resid 1328 through 1337 removed outlier: 3.571A pdb=" N GLU J1334 " --> pdb=" O ARG J1330 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1353 Processing helix chain 'J' and resid 1363 through 1372 Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 56 Processing helix chain 'K' and resid 61 through 77 Processing helix chain 'L' and resid 97 through 107 removed outlier: 4.508A pdb=" N THR L 107 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 136 removed outlier: 3.954A pdb=" N ILE L 117 " --> pdb=" O ARG L 113 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU L 136 " --> pdb=" O CYS L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 152 Processing helix chain 'L' and resid 214 through 234 Processing helix chain 'L' and resid 243 through 258 removed outlier: 4.185A pdb=" N GLU L 247 " --> pdb=" O ALA L 243 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU L 250 " --> pdb=" O GLN L 246 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU L 254 " --> pdb=" O LEU L 250 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL L 255 " --> pdb=" O LYS L 251 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN L 258 " --> pdb=" O GLU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 291 removed outlier: 3.647A pdb=" N ASP L 267 " --> pdb=" O PRO L 263 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR L 268 " --> pdb=" O LYS L 264 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET L 276 " --> pdb=" O SER L 272 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU L 286 " --> pdb=" O THR L 282 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET L 288 " --> pdb=" O GLU L 284 " (cutoff:3.500A) Processing helix chain 'L' and resid 299 through 304 Processing helix chain 'L' and resid 330 through 349 removed outlier: 4.402A pdb=" N GLU L 335 " --> pdb=" O HIS L 331 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLU L 336 " --> pdb=" O ASP L 332 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG L 339 " --> pdb=" O GLU L 335 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU L 348 " --> pdb=" O LEU L 344 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU L 349 " --> pdb=" O GLN L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 382 removed outlier: 4.230A pdb=" N ARG L 364 " --> pdb=" O ASP L 360 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA L 370 " --> pdb=" O SER L 366 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) Processing helix chain 'L' and resid 384 through 391 removed outlier: 3.675A pdb=" N ILE L 388 " --> pdb=" O LEU L 384 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 418 removed outlier: 3.533A pdb=" N GLU L 407 " --> pdb=" O ASP L 403 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN L 409 " --> pdb=" O ILE L 405 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE L 410 " --> pdb=" O GLN L 406 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP L 417 " --> pdb=" O MET L 413 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS L 418 " --> pdb=" O LYS L 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 421 through 423 No H-bonds generated for 'chain 'L' and resid 421 through 423' Processing helix chain 'L' and resid 427 through 446 removed outlier: 4.360A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP L 445 " --> pdb=" O ARG L 441 " (cutoff:3.500A) Processing helix chain 'L' and resid 454 through 469 removed outlier: 3.673A pdb=" N THR L 459 " --> pdb=" O HIS L 455 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS L 462 " --> pdb=" O GLU L 458 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG L 468 " --> pdb=" O ASN L 464 " (cutoff:3.500A) Processing helix chain 'L' and resid 471 through 474 No H-bonds generated for 'chain 'L' and resid 471 through 474' Processing helix chain 'L' and resid 480 through 487 removed outlier: 3.597A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 491 through 498 Processing helix chain 'L' and resid 519 through 522 Processing helix chain 'L' and resid 531 through 550 removed outlier: 3.593A pdb=" N GLU L 538 " --> pdb=" O SER L 534 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA L 542 " --> pdb=" O GLU L 538 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS L 545 " --> pdb=" O ARG L 541 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU L 548 " --> pdb=" O THR L 544 " (cutoff:3.500A) Processing helix chain 'L' and resid 555 through 562 removed outlier: 3.888A pdb=" N ARG L 560 " --> pdb=" O ALA L 556 " (cutoff:3.500A) Processing helix chain 'L' and resid 573 through 580 removed outlier: 3.613A pdb=" N LYS L 578 " --> pdb=" O GLU L 574 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN L 579 " --> pdb=" O GLU L 575 " (cutoff:3.500A) Processing helix chain 'L' and resid 584 through 599 Processing helix chain 'L' and resid 607 through 610 Processing helix chain 'R' and resid 257 through 260 removed outlier: 3.638A pdb=" N LEU R 260 " --> pdb=" O VAL R 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 257 through 260' Processing helix chain 'R' and resid 264 through 272 Processing helix chain 'R' and resid 278 through 283 Processing helix chain 'R' and resid 286 through 291 Processing helix chain 'R' and resid 297 through 309 Processing sheet with id= A, first strand: chain 'G' and resid 182 through 189 removed outlier: 3.525A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS G 23 " --> pdb=" O SER G 20 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS G 25 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLN G 18 " --> pdb=" O LYS G 25 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.742A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 107 through 111 Processing sheet with id= D, first strand: chain 'H' and resid 23 through 28 Processing sheet with id= E, first strand: chain 'H' and resid 90 through 92 Processing sheet with id= F, first strand: chain 'H' and resid 99 through 101 removed outlier: 3.513A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 109 through 111 Processing sheet with id= H, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= I, first strand: chain 'I' and resid 116 through 123 removed outlier: 3.948A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= K, first strand: chain 'I' and resid 148 through 151 Processing sheet with id= L, first strand: chain 'I' and resid 154 through 156 Processing sheet with id= M, first strand: chain 'I' and resid 184 through 188 Processing sheet with id= N, first strand: chain 'I' and resid 227 through 231 Processing sheet with id= O, first strand: chain 'I' and resid 603 through 607 Processing sheet with id= P, first strand: chain 'I' and resid 748 through 752 removed outlier: 3.678A pdb=" N ARG I 731 " --> pdb=" O ASP I 728 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 1226 through 1232 removed outlier: 4.443A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 887 through 889 Processing sheet with id= S, first strand: chain 'I' and resid 255 through 257 removed outlier: 3.803A pdb=" N VAL I 263 " --> pdb=" O ILE I 255 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 633 through 639 removed outlier: 6.272A pdb=" N GLU I 641 " --> pdb=" O SER I 638 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 816 through 819 removed outlier: 7.432A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.797A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 103 through 106 removed outlier: 3.626A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= Y, first strand: chain 'J' and resid 547 through 556 Processing sheet with id= Z, first strand: chain 'J' and resid 706 through 709 Processing sheet with id= AA, first strand: chain 'J' and resid 820 through 822 Processing sheet with id= AB, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.792A pdb=" N SER J 961 " --> pdb=" O GLU J 981 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 965 through 967 removed outlier: 3.658A pdb=" N VAL J 966 " --> pdb=" O VAL J 974 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id= AE, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.391A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP J1305 " --> pdb=" O LYS J1263 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.473A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) 910 hydrogen bonds defined for protein. 2652 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 116 hydrogen bonds 232 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 14.64 Time building geometry restraints manager: 13.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9968 1.34 - 1.46: 6351 1.46 - 1.58: 15936 1.58 - 1.70: 244 1.70 - 1.83: 235 Bond restraints: 32734 Sorted by residual: bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.827 -0.295 2.00e-02 2.50e+03 2.17e+02 bond pdb=" C19 1N7 G 401 " pdb=" C3 1N7 G 401 " ideal model delta sigma weight residual 1.532 1.821 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.819 -0.287 2.00e-02 2.50e+03 2.06e+02 bond pdb=" C3 1N7 J1504 " pdb=" C4 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.740 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C3 1N7 G 401 " pdb=" C4 1N7 G 401 " ideal model delta sigma weight residual 1.532 1.727 -0.195 2.00e-02 2.50e+03 9.54e+01 ... (remaining 32729 not shown) Histogram of bond angle deviations from ideal: 98.04 - 105.24: 1026 105.24 - 112.44: 16901 112.44 - 119.63: 11235 119.63 - 126.83: 14959 126.83 - 134.03: 601 Bond angle restraints: 44722 Sorted by residual: angle pdb=" N GLY I1261 " pdb=" CA GLY I1261 " pdb=" C GLY I1261 " ideal model delta sigma weight residual 111.03 120.21 -9.18 1.40e+00 5.10e-01 4.30e+01 angle pdb=" C LEU J 903 " pdb=" N ALA J 904 " pdb=" CA ALA J 904 " ideal model delta sigma weight residual 121.54 131.11 -9.57 1.91e+00 2.74e-01 2.51e+01 angle pdb=" N ILE L 367 " pdb=" CA ILE L 367 " pdb=" C ILE L 367 " ideal model delta sigma weight residual 111.81 107.72 4.09 8.60e-01 1.35e+00 2.27e+01 angle pdb=" C LEU I 484 " pdb=" N ASP I 485 " pdb=" CA ASP I 485 " ideal model delta sigma weight residual 121.70 129.63 -7.93 1.80e+00 3.09e-01 1.94e+01 angle pdb=" C ASP I 696 " pdb=" N LYS I 697 " pdb=" CA LYS I 697 " ideal model delta sigma weight residual 121.80 131.87 -10.07 2.44e+00 1.68e-01 1.70e+01 ... (remaining 44717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 19233 35.74 - 71.47: 783 71.47 - 107.21: 27 107.21 - 142.94: 2 142.94 - 178.68: 3 Dihedral angle restraints: 20048 sinusoidal: 9239 harmonic: 10809 Sorted by residual: dihedral pdb=" CA ALA J 904 " pdb=" C ALA J 904 " pdb=" N ARG J 905 " pdb=" CA ARG J 905 " ideal model delta harmonic sigma weight residual 180.00 147.49 32.51 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA SER I 398 " pdb=" C SER I 398 " pdb=" N ALA I 399 " pdb=" CA ALA I 399 " ideal model delta harmonic sigma weight residual 180.00 151.47 28.53 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA VAL K 32 " pdb=" C VAL K 32 " pdb=" N GLY K 33 " pdb=" CA GLY K 33 " ideal model delta harmonic sigma weight residual -180.00 -151.50 -28.50 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 20045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 4773 0.086 - 0.172: 336 0.172 - 0.257: 5 0.257 - 0.343: 5 0.343 - 0.429: 3 Chirality restraints: 5122 Sorted by residual: chirality pdb=" C19 1N7 J1504 " pdb=" C18 1N7 J1504 " pdb=" C2 1N7 J1504 " pdb=" C3 1N7 J1504 " both_signs ideal model delta sigma weight residual False -2.53 -2.96 0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" C19 1N7 G 401 " pdb=" C18 1N7 G 401 " pdb=" C2 1N7 G 401 " pdb=" C3 1N7 G 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.95 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.92 0.39 2.00e-01 2.50e+01 3.74e+00 ... (remaining 5119 not shown) Planarity restraints: 5408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS I 551 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO I 552 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO I 552 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO I 552 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE I 514 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C PHE I 514 " -0.036 2.00e-02 2.50e+03 pdb=" O PHE I 514 " 0.013 2.00e-02 2.50e+03 pdb=" N MET I 515 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS I 496 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO I 497 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO I 497 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO I 497 " -0.028 5.00e-02 4.00e+02 ... (remaining 5405 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 2326 2.74 - 3.28: 29953 3.28 - 3.82: 51085 3.82 - 4.36: 64212 4.36 - 4.90: 109374 Nonbonded interactions: 256950 Sorted by model distance: nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 2.195 2.170 nonbonded pdb=" OG1 THR I 843 " pdb=" O GLY I 846 " model vdw 2.248 2.440 nonbonded pdb=" O ILE I 11 " pdb=" OH TYR I1149 " model vdw 2.250 2.440 nonbonded pdb=" NH1 ARG I1246 " pdb=" OD1 ASP J 348 " model vdw 2.252 2.520 nonbonded pdb=" OG SER J 353 " pdb=" O LYS J 445 " model vdw 2.253 2.440 ... (remaining 256945 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 'G' and (resid 5 through 158 or resid 167 through 233)) selection = (chain 'H' and resid 5 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: 1.380 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: 8.890 Check model and map are aligned: 0.470 Set scattering table: 0.300 Process input model: 100.540 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 0.295 32734 Z= 0.383 Angle : 0.672 10.068 44722 Z= 0.395 Chirality : 0.046 0.429 5122 Planarity : 0.004 0.052 5408 Dihedral : 16.515 178.678 13078 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.36 % Favored : 94.61 % Rotamer: Outliers : 3.83 % Allowed : 8.24 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.13), residues: 3730 helix: -1.10 (0.13), residues: 1444 sheet: -1.02 (0.25), residues: 417 loop : -1.48 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J1193 HIS 0.006 0.001 HIS I 447 PHE 0.013 0.002 PHE K 17 TYR 0.013 0.002 TYR I1281 ARG 0.004 0.000 ARG J 610 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 347 time to evaluate : 3.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 38 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7477 (t) REVERT: H 114 ASP cc_start: 0.7972 (m-30) cc_final: 0.7599 (m-30) REVERT: H 183 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8558 (tp) REVERT: I 119 GLU cc_start: 0.8598 (tt0) cc_final: 0.8324 (tt0) REVERT: I 189 ASP cc_start: 0.7057 (p0) cc_final: 0.6796 (p0) REVERT: I 200 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7904 (mmm-85) REVERT: I 342 ASP cc_start: 0.8287 (t0) cc_final: 0.8054 (t70) REVERT: I 365 GLU cc_start: 0.6905 (tp30) cc_final: 0.6631 (tp30) REVERT: I 538 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8102 (pp) REVERT: I 859 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7574 (tp30) REVERT: I 895 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7280 (pp) REVERT: J 151 MET cc_start: 0.6302 (OUTLIER) cc_final: 0.5483 (ppp) REVERT: J 320 ASN cc_start: 0.7467 (m-40) cc_final: 0.7257 (m-40) REVERT: J 992 LYS cc_start: 0.7378 (tppp) cc_final: 0.6565 (tppp) REVERT: J 1189 MET cc_start: 0.7388 (mmp) cc_final: 0.7182 (mmp) REVERT: K 56 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7677 (mt-10) REVERT: L 104 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7455 (mm-30) REVERT: L 137 TYR cc_start: 0.6521 (OUTLIER) cc_final: 0.5552 (m-80) REVERT: L 149 ASP cc_start: 0.3748 (OUTLIER) cc_final: 0.3540 (m-30) REVERT: L 261 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6846 (tt) REVERT: L 468 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7777 (ptt-90) REVERT: L 489 MET cc_start: 0.8480 (ptp) cc_final: 0.8081 (ptp) outliers start: 123 outliers final: 55 residues processed: 443 average time/residue: 1.3355 time to fit residues: 709.0615 Evaluate side-chains 342 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 275 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 859 GLU Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 261 LEU Chi-restraints excluded: chain L residue 468 ARG Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 8.9990 chunk 291 optimal weight: 5.9990 chunk 161 optimal weight: 0.0770 chunk 99 optimal weight: 5.9990 chunk 196 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 348 optimal weight: 5.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 103 ASN H 186 ASN I 83 GLN I 193 ASN I 649 GLN I 799 ASN J 300 GLN J 792 ASN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1227 HIS L 342 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32734 Z= 0.197 Angle : 0.535 7.846 44722 Z= 0.284 Chirality : 0.041 0.205 5122 Planarity : 0.004 0.046 5408 Dihedral : 17.367 179.035 5753 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.14 % Allowed : 11.20 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.13), residues: 3730 helix: -0.35 (0.14), residues: 1454 sheet: -0.81 (0.26), residues: 408 loop : -1.41 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J1193 HIS 0.005 0.001 HIS I 447 PHE 0.012 0.001 PHE J 620 TYR 0.011 0.001 TYR J 679 ARG 0.004 0.000 ARG J1231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 311 time to evaluate : 3.389 Fit side-chains revert: symmetry clash REVERT: H 13 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6717 (pp) REVERT: H 183 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8487 (tp) REVERT: H 226 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7611 (mt-10) REVERT: I 189 ASP cc_start: 0.6902 (p0) cc_final: 0.6696 (p0) REVERT: I 200 ARG cc_start: 0.8251 (mtp85) cc_final: 0.8002 (mmm-85) REVERT: I 202 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7853 (ttp80) REVERT: I 365 GLU cc_start: 0.6815 (tp30) cc_final: 0.6541 (tp30) REVERT: I 412 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6509 (pm20) REVERT: I 514 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7263 (m-80) REVERT: I 538 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8236 (pp) REVERT: I 681 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7500 (mtt) REVERT: I 895 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7421 (pp) REVERT: I 1107 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8160 (mtp) REVERT: I 1154 ASP cc_start: 0.7484 (t0) cc_final: 0.7167 (t0) REVERT: J 151 MET cc_start: 0.6203 (OUTLIER) cc_final: 0.5241 (ppp) REVERT: J 163 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: J 413 ASP cc_start: 0.7521 (m-30) cc_final: 0.7245 (m-30) REVERT: J 603 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7434 (pttp) REVERT: J 992 LYS cc_start: 0.7520 (tppp) cc_final: 0.6716 (tppp) REVERT: J 1189 MET cc_start: 0.7419 (mmp) cc_final: 0.7211 (mmp) REVERT: J 1231 ARG cc_start: 0.7034 (mtp85) cc_final: 0.6377 (mtt180) REVERT: K 55 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7419 (mt-10) REVERT: K 68 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6458 (tt0) REVERT: L 104 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7207 (mm-30) REVERT: L 137 TYR cc_start: 0.6689 (OUTLIER) cc_final: 0.5257 (m-80) REVERT: L 261 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6946 (tt) REVERT: L 274 ARG cc_start: 0.7660 (mtt-85) cc_final: 0.7275 (mmm160) REVERT: L 489 MET cc_start: 0.8468 (ptp) cc_final: 0.8049 (ptp) outliers start: 133 outliers final: 65 residues processed: 400 average time/residue: 1.3846 time to fit residues: 661.7962 Evaluate side-chains 371 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 291 time to evaluate : 3.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 603 LYS Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 234 THR Chi-restraints excluded: chain L residue 261 LEU Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 569 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 0.8980 chunk 108 optimal weight: 0.0870 chunk 290 optimal weight: 0.7980 chunk 237 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 349 optimal weight: 0.4980 chunk 377 optimal weight: 0.0470 chunk 311 optimal weight: 4.9990 chunk 346 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 103 ASN I 193 ASN I 649 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 131 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 32734 Z= 0.131 Angle : 0.482 7.653 44722 Z= 0.256 Chirality : 0.039 0.203 5122 Planarity : 0.003 0.041 5408 Dihedral : 16.785 179.601 5720 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.48 % Allowed : 12.91 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3730 helix: 0.23 (0.14), residues: 1457 sheet: -0.66 (0.25), residues: 432 loop : -1.33 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 33 HIS 0.004 0.001 HIS J 651 PHE 0.013 0.001 PHE G 8 TYR 0.012 0.001 TYR H 152 ARG 0.005 0.000 ARG L 596 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 321 time to evaluate : 3.584 Fit side-chains revert: symmetry clash REVERT: G 204 GLU cc_start: 0.7565 (tt0) cc_final: 0.7271 (mt-10) REVERT: I 189 ASP cc_start: 0.6820 (p0) cc_final: 0.6617 (p0) REVERT: I 200 ARG cc_start: 0.8193 (mtp85) cc_final: 0.7949 (mmm-85) REVERT: I 222 ASP cc_start: 0.7269 (t0) cc_final: 0.7019 (t0) REVERT: I 365 GLU cc_start: 0.6722 (tp30) cc_final: 0.6483 (tp30) REVERT: I 473 ARG cc_start: 0.6854 (mtp180) cc_final: 0.6628 (mtm180) REVERT: I 514 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7287 (m-80) REVERT: I 538 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8490 (pp) REVERT: I 681 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7500 (mtt) REVERT: I 895 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7435 (pp) REVERT: I 1143 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7025 (tp30) REVERT: I 1154 ASP cc_start: 0.7441 (t0) cc_final: 0.7133 (t0) REVERT: J 151 MET cc_start: 0.6151 (OUTLIER) cc_final: 0.5238 (ppp) REVERT: J 163 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: J 314 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6777 (ptt180) REVERT: J 992 LYS cc_start: 0.7473 (tppp) cc_final: 0.6694 (tppp) REVERT: J 1189 MET cc_start: 0.7382 (mmp) cc_final: 0.7162 (mmp) REVERT: J 1231 ARG cc_start: 0.7006 (mtp85) cc_final: 0.6768 (ttm110) REVERT: K 55 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7348 (mt-10) REVERT: L 104 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: L 261 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7067 (tt) REVERT: L 274 ARG cc_start: 0.7675 (mtt-85) cc_final: 0.7302 (mmm160) REVERT: L 489 MET cc_start: 0.8385 (ptp) cc_final: 0.8106 (ptp) REVERT: L 568 ASN cc_start: 0.7372 (m110) cc_final: 0.7134 (t0) REVERT: R 260 LEU cc_start: 0.5100 (OUTLIER) cc_final: 0.4133 (mt) outliers start: 112 outliers final: 51 residues processed: 391 average time/residue: 1.4490 time to fit residues: 675.5654 Evaluate side-chains 349 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 287 time to evaluate : 3.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 234 THR Chi-restraints excluded: chain L residue 261 LEU Chi-restraints excluded: chain L residue 468 ARG Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain R residue 260 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 5.9990 chunk 262 optimal weight: 2.9990 chunk 181 optimal weight: 0.0050 chunk 38 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 234 optimal weight: 4.9990 chunk 350 optimal weight: 3.9990 chunk 371 optimal weight: 10.0000 chunk 183 optimal weight: 0.7980 chunk 332 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN I 193 ASN I 343 HIS I 649 GLN I 725 GLN I1038 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 32734 Z= 0.293 Angle : 0.551 9.171 44722 Z= 0.288 Chirality : 0.042 0.221 5122 Planarity : 0.004 0.045 5408 Dihedral : 16.831 179.426 5701 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.20 % Allowed : 13.59 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3730 helix: 0.18 (0.14), residues: 1471 sheet: -0.63 (0.26), residues: 416 loop : -1.28 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 868 HIS 0.006 0.001 HIS I 447 PHE 0.014 0.001 PHE J 620 TYR 0.013 0.001 TYR I1231 ARG 0.007 0.000 ARG L 596 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 286 time to evaluate : 3.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 62 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7358 (t0) REVERT: H 13 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6747 (pp) REVERT: H 38 THR cc_start: 0.7978 (OUTLIER) cc_final: 0.7485 (t) REVERT: I 200 ARG cc_start: 0.8243 (mtp85) cc_final: 0.7976 (mmm-85) REVERT: I 342 ASP cc_start: 0.8244 (t0) cc_final: 0.7947 (t70) REVERT: I 538 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8573 (pp) REVERT: I 681 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7863 (mtt) REVERT: I 761 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.7537 (mm110) REVERT: I 895 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7534 (pp) REVERT: I 1143 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7068 (tp30) REVERT: I 1154 ASP cc_start: 0.7529 (t0) cc_final: 0.7207 (t0) REVERT: J 151 MET cc_start: 0.6066 (OUTLIER) cc_final: 0.5270 (ppp) REVERT: J 163 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: J 314 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7016 (ptt180) REVERT: J 992 LYS cc_start: 0.7524 (tppp) cc_final: 0.6554 (tppp) REVERT: K 55 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7353 (mt-10) REVERT: K 68 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6467 (tt0) REVERT: L 104 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7405 (mm-30) REVERT: L 274 ARG cc_start: 0.7741 (mtt-85) cc_final: 0.7252 (mmm160) REVERT: L 489 MET cc_start: 0.8436 (ptp) cc_final: 0.8125 (ptp) REVERT: R 260 LEU cc_start: 0.5181 (pt) cc_final: 0.4107 (mt) outliers start: 135 outliers final: 76 residues processed: 386 average time/residue: 1.3605 time to fit residues: 629.2731 Evaluate side-chains 366 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 277 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 168 ILE Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 596 ASP Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 761 GLN Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 234 THR Chi-restraints excluded: chain L residue 468 ARG Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 587 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 0.1980 chunk 210 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 276 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 316 optimal weight: 3.9990 chunk 256 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 333 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 103 ASN I 193 ASN I 649 GLN I1038 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 362 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32734 Z= 0.205 Angle : 0.516 11.301 44722 Z= 0.271 Chirality : 0.041 0.213 5122 Planarity : 0.004 0.044 5408 Dihedral : 16.740 179.007 5699 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.98 % Allowed : 14.53 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3730 helix: 0.37 (0.14), residues: 1472 sheet: -0.50 (0.26), residues: 411 loop : -1.23 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 686 HIS 0.004 0.001 HIS I 447 PHE 0.011 0.001 PHE I 514 TYR 0.014 0.001 TYR I 70 ARG 0.007 0.000 ARG L 596 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 288 time to evaluate : 3.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 62 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7308 (t0) REVERT: G 183 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8831 (mm) REVERT: H 13 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6682 (pp) REVERT: H 38 THR cc_start: 0.7877 (OUTLIER) cc_final: 0.7155 (t) REVERT: H 183 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8455 (tp) REVERT: I 200 ARG cc_start: 0.8235 (mtp85) cc_final: 0.7969 (mmm-85) REVERT: I 342 ASP cc_start: 0.8248 (t0) cc_final: 0.7943 (t70) REVERT: I 473 ARG cc_start: 0.6954 (mtp180) cc_final: 0.6661 (mtm180) REVERT: I 514 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7448 (m-80) REVERT: I 538 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8579 (pp) REVERT: I 895 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7513 (pp) REVERT: I 1143 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7053 (tp30) REVERT: I 1154 ASP cc_start: 0.7554 (t0) cc_final: 0.7247 (t0) REVERT: J 151 MET cc_start: 0.6087 (OUTLIER) cc_final: 0.5199 (ppp) REVERT: J 163 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: J 314 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6995 (ptt180) REVERT: J 684 ASP cc_start: 0.7409 (m-30) cc_final: 0.7079 (m-30) REVERT: J 992 LYS cc_start: 0.7525 (tppp) cc_final: 0.6554 (tppp) REVERT: J 1231 ARG cc_start: 0.7059 (mtp85) cc_final: 0.6387 (mtt180) REVERT: K 55 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7377 (mt-10) REVERT: K 68 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6455 (tt0) REVERT: L 104 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7457 (mm-30) REVERT: L 265 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.6772 (tp40) REVERT: L 274 ARG cc_start: 0.7745 (mtt-85) cc_final: 0.7263 (mmm160) REVERT: L 362 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7376 (m110) REVERT: L 364 ARG cc_start: 0.7953 (mtm110) cc_final: 0.6955 (ptp-170) REVERT: L 489 MET cc_start: 0.8394 (ptp) cc_final: 0.8079 (ptp) REVERT: R 260 LEU cc_start: 0.5112 (OUTLIER) cc_final: 0.4126 (mt) outliers start: 128 outliers final: 69 residues processed: 382 average time/residue: 1.3753 time to fit residues: 630.3405 Evaluate side-chains 368 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 282 time to evaluate : 3.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1284 ARG Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 234 THR Chi-restraints excluded: chain L residue 265 GLN Chi-restraints excluded: chain L residue 362 ASN Chi-restraints excluded: chain L residue 468 ARG Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain R residue 260 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 2.9990 chunk 334 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 371 optimal weight: 10.0000 chunk 308 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 195 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN I 193 ASN I 214 ASN I 649 GLN I 932 GLN I1038 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 131 GLN L 362 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 32734 Z= 0.229 Angle : 0.524 12.648 44722 Z= 0.274 Chirality : 0.041 0.211 5122 Planarity : 0.004 0.044 5408 Dihedral : 16.725 178.734 5698 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.57 % Allowed : 14.46 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3730 helix: 0.42 (0.14), residues: 1471 sheet: -0.46 (0.26), residues: 411 loop : -1.23 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 868 HIS 0.004 0.001 HIS I 447 PHE 0.012 0.001 PHE I 514 TYR 0.011 0.001 TYR J1365 ARG 0.008 0.000 ARG G 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 288 time to evaluate : 3.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 62 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7310 (t0) REVERT: H 13 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6689 (pp) REVERT: H 183 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8440 (tp) REVERT: I 200 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7981 (mmm-85) REVERT: I 214 ASN cc_start: 0.8455 (t0) cc_final: 0.8251 (t0) REVERT: I 342 ASP cc_start: 0.8258 (t0) cc_final: 0.7950 (t70) REVERT: I 412 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6578 (pm20) REVERT: I 473 ARG cc_start: 0.6981 (mtp180) cc_final: 0.6690 (mtm180) REVERT: I 514 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7478 (m-80) REVERT: I 538 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8581 (pp) REVERT: I 761 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.7556 (mm110) REVERT: I 859 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7404 (tp30) REVERT: I 895 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7505 (pp) REVERT: I 1143 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7058 (tp30) REVERT: I 1154 ASP cc_start: 0.7555 (t0) cc_final: 0.7272 (t0) REVERT: J 151 MET cc_start: 0.5973 (OUTLIER) cc_final: 0.5204 (ppp) REVERT: J 163 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: J 314 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.7013 (ptt180) REVERT: J 684 ASP cc_start: 0.7409 (m-30) cc_final: 0.7075 (m-30) REVERT: J 992 LYS cc_start: 0.7535 (tppp) cc_final: 0.6559 (tppp) REVERT: J 1025 MET cc_start: 0.6487 (OUTLIER) cc_final: 0.5532 (mtt) REVERT: J 1152 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7412 (tm-30) REVERT: J 1231 ARG cc_start: 0.7014 (mtp85) cc_final: 0.6362 (mtt180) REVERT: K 55 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7382 (mt-10) REVERT: K 68 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6458 (tt0) REVERT: L 104 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7449 (mm-30) REVERT: L 265 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.6760 (tp-100) REVERT: L 274 ARG cc_start: 0.7773 (mtt-85) cc_final: 0.7272 (mmm160) REVERT: L 364 ARG cc_start: 0.8078 (mtm110) cc_final: 0.7616 (ptp-170) REVERT: L 489 MET cc_start: 0.8406 (ptp) cc_final: 0.8089 (ptp) REVERT: R 260 LEU cc_start: 0.5101 (OUTLIER) cc_final: 0.4125 (mt) outliers start: 147 outliers final: 88 residues processed: 393 average time/residue: 1.3570 time to fit residues: 641.6384 Evaluate side-chains 388 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 282 time to evaluate : 3.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 168 ILE Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 761 GLN Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 859 GLU Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1284 ARG Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 234 THR Chi-restraints excluded: chain L residue 265 GLN Chi-restraints excluded: chain L residue 468 ARG Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain R residue 260 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 211 optimal weight: 0.0370 chunk 271 optimal weight: 5.9990 chunk 210 optimal weight: 0.5980 chunk 312 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 370 optimal weight: 10.0000 chunk 231 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 170 optimal weight: 0.5980 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN I 193 ASN I 649 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 131 GLN L 362 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32734 Z= 0.196 Angle : 0.513 11.932 44722 Z= 0.269 Chirality : 0.040 0.210 5122 Planarity : 0.003 0.043 5408 Dihedral : 16.663 178.310 5698 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.39 % Allowed : 14.81 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3730 helix: 0.59 (0.14), residues: 1461 sheet: -0.48 (0.25), residues: 420 loop : -1.19 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 321 HIS 0.004 0.001 HIS J 651 PHE 0.012 0.001 PHE I 337 TYR 0.011 0.001 TYR H 152 ARG 0.005 0.000 ARG L 596 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 289 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 62 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7281 (t0) REVERT: H 13 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6671 (pp) REVERT: H 183 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8440 (tp) REVERT: I 200 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7982 (mmm-85) REVERT: I 342 ASP cc_start: 0.8257 (t0) cc_final: 0.7948 (t70) REVERT: I 412 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6566 (pm20) REVERT: I 473 ARG cc_start: 0.6972 (mtp180) cc_final: 0.6684 (mtm180) REVERT: I 514 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7466 (m-80) REVERT: I 538 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8570 (pp) REVERT: I 681 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7495 (mtt) REVERT: I 859 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7390 (tp30) REVERT: I 895 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7462 (pp) REVERT: I 1143 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7046 (tp30) REVERT: I 1154 ASP cc_start: 0.7560 (t0) cc_final: 0.7286 (t0) REVERT: J 151 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.5215 (ppp) REVERT: J 163 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: J 314 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7007 (ptt180) REVERT: J 684 ASP cc_start: 0.7397 (m-30) cc_final: 0.7067 (m-30) REVERT: J 992 LYS cc_start: 0.7524 (tppp) cc_final: 0.6543 (tppp) REVERT: J 1025 MET cc_start: 0.6478 (OUTLIER) cc_final: 0.5531 (mtt) REVERT: J 1152 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7593 (tm-30) REVERT: J 1231 ARG cc_start: 0.6991 (mtp85) cc_final: 0.6766 (ttm110) REVERT: K 55 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7361 (mt-10) REVERT: K 68 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6453 (tt0) REVERT: L 96 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6851 (t0) REVERT: L 104 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7454 (mm-30) REVERT: L 364 ARG cc_start: 0.8001 (mtm110) cc_final: 0.7518 (ptp-170) REVERT: L 489 MET cc_start: 0.8391 (ptp) cc_final: 0.8105 (ptp) REVERT: R 260 LEU cc_start: 0.5107 (OUTLIER) cc_final: 0.4166 (mt) REVERT: R 295 LEU cc_start: 0.3916 (OUTLIER) cc_final: 0.3409 (mp) outliers start: 141 outliers final: 87 residues processed: 389 average time/residue: 1.3510 time to fit residues: 627.9948 Evaluate side-chains 389 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 283 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 168 ILE Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 596 ASP Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 859 GLU Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1284 ARG Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 468 ARG Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 72 optimal weight: 0.0870 chunk 71 optimal weight: 4.9990 chunk 235 optimal weight: 0.3980 chunk 252 optimal weight: 0.9980 chunk 182 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN I 214 ASN I 649 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 362 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32734 Z= 0.159 Angle : 0.494 10.740 44722 Z= 0.260 Chirality : 0.040 0.201 5122 Planarity : 0.003 0.043 5408 Dihedral : 16.555 177.738 5696 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.79 % Allowed : 15.52 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % 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: -0.49 (0.14), residues: 3730 helix: 0.76 (0.14), residues: 1462 sheet: -0.51 (0.25), residues: 425 loop : -1.15 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 33 HIS 0.003 0.001 HIS J 651 PHE 0.010 0.001 PHE I 514 TYR 0.011 0.001 TYR I 70 ARG 0.008 0.000 ARG L 596 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 297 time to evaluate : 3.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 12 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7317 (ptp90) REVERT: G 204 GLU cc_start: 0.7541 (tt0) cc_final: 0.7219 (mt-10) REVERT: H 13 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6649 (pp) REVERT: H 206 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7623 (pt0) REVERT: I 200 ARG cc_start: 0.8225 (mtp85) cc_final: 0.7974 (mmm-85) REVERT: I 342 ASP cc_start: 0.8261 (t0) cc_final: 0.7961 (t70) REVERT: I 473 ARG cc_start: 0.6953 (mtp180) cc_final: 0.6738 (mtm180) REVERT: I 514 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7366 (m-80) REVERT: I 538 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8605 (pp) REVERT: I 859 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7379 (tp30) REVERT: I 895 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7455 (pp) REVERT: I 1143 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7024 (tp30) REVERT: I 1154 ASP cc_start: 0.7561 (t0) cc_final: 0.7297 (t0) REVERT: J 81 ARG cc_start: 0.7717 (ttp-110) cc_final: 0.7384 (ttp80) REVERT: J 151 MET cc_start: 0.5775 (OUTLIER) cc_final: 0.5146 (ppp) REVERT: J 163 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: J 314 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7004 (ptt180) REVERT: J 684 ASP cc_start: 0.7389 (m-30) cc_final: 0.7051 (m-30) REVERT: J 992 LYS cc_start: 0.7512 (tppp) cc_final: 0.6528 (tppp) REVERT: J 1025 MET cc_start: 0.6495 (OUTLIER) cc_final: 0.5544 (mtt) REVERT: J 1152 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7543 (tm-30) REVERT: K 55 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7366 (mt-10) REVERT: K 56 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7262 (mt-10) REVERT: K 68 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6428 (tt0) REVERT: L 104 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7278 (mm-30) REVERT: L 273 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6540 (tmt) REVERT: L 288 MET cc_start: 0.4153 (tpp) cc_final: 0.3916 (ptp) REVERT: L 362 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7289 (m110) REVERT: L 364 ARG cc_start: 0.8073 (mtm110) cc_final: 0.7709 (ptp-170) REVERT: L 476 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8287 (pmt-80) REVERT: L 489 MET cc_start: 0.8396 (ptp) cc_final: 0.8127 (ptp) REVERT: R 260 LEU cc_start: 0.4903 (OUTLIER) cc_final: 0.4000 (mt) REVERT: R 295 LEU cc_start: 0.4041 (OUTLIER) cc_final: 0.3555 (mp) outliers start: 122 outliers final: 72 residues processed: 383 average time/residue: 1.4331 time to fit residues: 654.1124 Evaluate side-chains 377 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 285 time to evaluate : 3.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 168 ILE Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 859 GLU Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 273 MET Chi-restraints excluded: chain L residue 362 ASN Chi-restraints excluded: chain L residue 468 ARG Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 2.9990 chunk 354 optimal weight: 7.9990 chunk 323 optimal weight: 2.9990 chunk 344 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 270 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 311 optimal weight: 4.9990 chunk 326 optimal weight: 9.9990 chunk 343 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN I 214 ASN I 649 GLN I 799 ASN J 335 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 362 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 32734 Z= 0.323 Angle : 0.577 10.689 44722 Z= 0.298 Chirality : 0.043 0.210 5122 Planarity : 0.004 0.045 5408 Dihedral : 16.709 177.714 5691 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.32 % Allowed : 15.09 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3730 helix: 0.48 (0.14), residues: 1473 sheet: -0.40 (0.25), residues: 417 loop : -1.20 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 868 HIS 0.007 0.001 HIS I 447 PHE 0.014 0.002 PHE J 380 TYR 0.016 0.001 TYR H 152 ARG 0.009 0.000 ARG L 596 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 278 time to evaluate : 3.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 12 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7484 (ptp90) REVERT: H 13 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6750 (pp) REVERT: H 183 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8480 (tp) REVERT: I 200 ARG cc_start: 0.8241 (mtp85) cc_final: 0.7976 (mmm-85) REVERT: I 342 ASP cc_start: 0.8252 (t0) cc_final: 0.7930 (t70) REVERT: I 412 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6544 (pm20) REVERT: I 473 ARG cc_start: 0.7015 (mtp180) cc_final: 0.6713 (mtm180) REVERT: I 538 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8576 (pp) REVERT: I 859 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7395 (tp30) REVERT: I 895 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7562 (pp) REVERT: I 1143 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7079 (tp30) REVERT: I 1180 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8140 (ttm) REVERT: J 151 MET cc_start: 0.5673 (OUTLIER) cc_final: 0.5107 (ppp) REVERT: J 163 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: J 314 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7028 (ptt180) REVERT: J 684 ASP cc_start: 0.7473 (m-30) cc_final: 0.7019 (m-30) REVERT: J 992 LYS cc_start: 0.7568 (tppp) cc_final: 0.6573 (tppp) REVERT: J 1152 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7584 (tm-30) REVERT: K 55 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7355 (mt-10) REVERT: K 56 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7291 (mt-10) REVERT: L 96 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.6947 (t0) REVERT: L 104 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7369 (mm-30) REVERT: L 273 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.6546 (tmt) REVERT: L 362 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7465 (m110) REVERT: L 364 ARG cc_start: 0.8154 (mtm110) cc_final: 0.7768 (ptp-170) REVERT: L 476 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8231 (pmt-80) REVERT: L 489 MET cc_start: 0.8454 (ptp) cc_final: 0.8141 (ptp) REVERT: R 260 LEU cc_start: 0.4937 (OUTLIER) cc_final: 0.3950 (mt) REVERT: R 295 LEU cc_start: 0.4090 (OUTLIER) cc_final: 0.3587 (mp) outliers start: 139 outliers final: 81 residues processed: 377 average time/residue: 1.4106 time to fit residues: 635.0757 Evaluate side-chains 380 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 279 time to evaluate : 3.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 859 GLU Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1113 LEU Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1180 MET Chi-restraints excluded: chain I residue 1192 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1284 ARG Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 273 MET Chi-restraints excluded: chain L residue 362 ASN Chi-restraints excluded: chain L residue 468 ARG Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 2.9990 chunk 364 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 382 optimal weight: 9.9990 chunk 352 optimal weight: 0.9990 chunk 304 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 235 optimal weight: 0.6980 chunk 186 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN I 214 ASN I 649 GLN I 799 ASN J 335 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 362 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32734 Z= 0.169 Angle : 0.515 10.740 44722 Z= 0.269 Chirality : 0.040 0.203 5122 Planarity : 0.003 0.042 5408 Dihedral : 16.616 177.626 5689 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.20 % Allowed : 16.36 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3730 helix: 0.73 (0.14), residues: 1461 sheet: -0.32 (0.26), residues: 410 loop : -1.13 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I1276 HIS 0.003 0.001 HIS J 651 PHE 0.013 0.001 PHE I 645 TYR 0.011 0.001 TYR I 70 ARG 0.009 0.000 ARG L 596 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 290 time to evaluate : 3.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 62 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.7193 (t0) REVERT: H 183 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8468 (tp) REVERT: I 200 ARG cc_start: 0.8212 (mtp85) cc_final: 0.7963 (mmm-85) REVERT: I 342 ASP cc_start: 0.8237 (t0) cc_final: 0.7925 (t70) REVERT: I 412 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6535 (pm20) REVERT: I 473 ARG cc_start: 0.6957 (mtp180) cc_final: 0.6746 (mtm180) REVERT: I 514 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: I 538 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8602 (pp) REVERT: I 859 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7374 (tp30) REVERT: I 895 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7462 (pp) REVERT: I 1143 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7041 (tp30) REVERT: I 1154 ASP cc_start: 0.7649 (t0) cc_final: 0.7329 (t0) REVERT: I 1180 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8144 (ttm) REVERT: J 151 MET cc_start: 0.5661 (OUTLIER) cc_final: 0.5144 (ppp) REVERT: J 163 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: J 314 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7046 (ptt180) REVERT: J 668 PHE cc_start: 0.6682 (t80) cc_final: 0.6473 (t80) REVERT: J 684 ASP cc_start: 0.7467 (m-30) cc_final: 0.7141 (m-30) REVERT: J 992 LYS cc_start: 0.7541 (tppp) cc_final: 0.6555 (tppp) REVERT: J 1152 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7607 (tm-30) REVERT: K 55 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7354 (mt-10) REVERT: L 96 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6836 (t0) REVERT: L 104 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7399 (mm-30) REVERT: L 362 ASN cc_start: 0.7853 (OUTLIER) cc_final: 0.7383 (m110) REVERT: L 364 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7452 (ptp-170) REVERT: L 476 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8224 (pmt-80) REVERT: L 489 MET cc_start: 0.8409 (ptp) cc_final: 0.8123 (ptp) REVERT: R 260 LEU cc_start: 0.4985 (OUTLIER) cc_final: 0.4022 (mt) REVERT: R 295 LEU cc_start: 0.4159 (OUTLIER) cc_final: 0.3660 (mp) outliers start: 103 outliers final: 69 residues processed: 365 average time/residue: 1.4140 time to fit residues: 613.4543 Evaluate side-chains 372 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 285 time to evaluate : 3.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 168 ILE Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 859 GLU Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1180 MET Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1284 ARG Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 362 ASN Chi-restraints excluded: chain L residue 468 ARG Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 6.9990 chunk 324 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 280 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 305 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 313 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN I 214 ASN I 649 GLN I 799 ASN I1116 HIS J 335 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.198660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.129579 restraints weight = 34122.332| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.21 r_work: 0.3252 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 32734 Z= 0.308 Angle : 0.574 16.066 44722 Z= 0.295 Chirality : 0.042 0.208 5122 Planarity : 0.004 0.044 5408 Dihedral : 16.681 177.680 5689 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.30 % Allowed : 16.27 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3730 helix: 0.52 (0.14), residues: 1472 sheet: -0.38 (0.26), residues: 418 loop : -1.16 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 868 HIS 0.006 0.001 HIS I 447 PHE 0.013 0.001 PHE I 514 TYR 0.013 0.001 TYR I 70 ARG 0.009 0.000 ARG L 596 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11254.00 seconds wall clock time: 200 minutes 49.78 seconds (12049.78 seconds total)