Starting phenix.real_space_refine on Wed Sep 25 22:08:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvs_41650/09_2024/8tvs_41650.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvs_41650/09_2024/8tvs_41650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvs_41650/09_2024/8tvs_41650.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvs_41650/09_2024/8tvs_41650.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvs_41650/09_2024/8tvs_41650.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvs_41650/09_2024/8tvs_41650.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.209 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: 8 Type Number sf(0) Gaussians Zn 8 6.06 5 P 104 5.49 5 Mg 1 5.21 5 S 157 5.16 5 C 19670 2.51 5 N 5698 2.21 5 O 6304 1.98 5 H 24971 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 56913 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 19036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 19036 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1254} Chain breaks: 4 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 491 Unresolved non-hydrogen angles: 630 Unresolved non-hydrogen dihedrals: 400 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 19, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 267 Chain: "B" Number of atoms: 14671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 14671 Classifications: {'peptide': 1041} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 45, 'TRANS': 995} Chain breaks: 10 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 581 Unresolved non-hydrogen angles: 739 Unresolved non-hydrogen dihedrals: 493 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 8, 'TYR:plan': 10, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 10, 'GLU:plan': 14, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 321 Chain: "C" Number of atoms: 4149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 4149 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1574 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 1 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'TYR%COO:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 114 Chain: "E" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3548 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1330 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "G" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1730 Classifications: {'peptide': 171} Modifications used: {'COO': 1, 'NH3': 1} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 127 Chain: "H" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2090 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 2 Chain: "I" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 972 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 175 Chain: "J" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1074 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1673 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "L" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 752 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "M" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 2171 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 433} Link IDs: {'CIS': 1, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 867 Unresolved non-hydrogen angles: 1300 Unresolved non-hydrogen dihedrals: 434 Planarities with less than four sites: {'UNK:plan-1': 433} Unresolved non-hydrogen planarities: 433 Chain: "N" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 946 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "T" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 925 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "R" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 263 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 3} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2450 SG CYS A 167 79.194 104.556 49.591 1.00173.20 S ATOM 946 SG CYS A 70 75.022 56.018 54.735 1.00129.41 S ATOM 1041 SG CYS A 77 74.076 55.490 58.660 1.00110.33 S ATOM 32713 SG CYS B1163 86.572 64.980 52.773 1.00132.71 S ATOM 33000 SG CYS B1182 83.289 64.887 52.278 1.00127.39 S ATOM 33039 SG CYS B1185 84.541 67.270 51.386 1.00129.48 S ATOM 35145 SG CYS C 95 60.548 14.739 109.907 1.00126.06 S ATOM 48920 SG CYS I 103 54.990 112.406 139.672 1.00147.56 S ATOM 48959 SG CYS I 106 54.345 115.855 138.817 1.00148.47 S ATOM 49255 SG CYS J 10 63.243 39.990 130.537 1.00 84.70 S ATOM 49811 SG CYS J 45 63.651 41.977 131.110 1.00 88.21 S ATOM 49821 SG CYS J 46 60.834 40.062 131.180 1.00 90.71 S ATOM 51957 SG CYS L 31 27.119 42.752 97.071 1.00134.59 S ATOM 52252 SG CYS L 51 25.183 44.315 98.560 1.00127.04 S Time building chain proxies: 20.78, per 1000 atoms: 0.37 Number of scatterers: 56913 At special positions: 0 Unit cell: (154.28, 158.92, 165.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 8 29.99 S 157 16.00 P 104 15.00 Mg 1 11.99 O 6304 8.00 N 5698 7.00 C 19670 6.00 H 24971 1.00 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 - 3.00 Amino acid : True - 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: 12.83 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7810 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 42 sheets defined 48.0% alpha, 18.1% beta 32 base pairs and 77 stacking pairs defined. Time for finding SS restraints: 22.61 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 removed outlier: 3.577A pdb=" N LEU A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 223 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 285 through 305 removed outlier: 3.995A pdb=" N GLU A 291 " --> pdb=" O HIS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 416 through 423 removed outlier: 6.543A pdb=" N LYS A 419 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG A 420 " --> pdb=" O TYR A 417 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA A 421 " --> pdb=" O SER A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 471 through 473 No H-bonds generated for 'chain 'A' and resid 471 through 473' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.682A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 506 through 511 Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.645A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.695A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.874A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 638 removed outlier: 3.529A pdb=" N VAL A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 634 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG A 635 " --> pdb=" O HIS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 659 removed outlier: 4.627A pdb=" N LYS A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 651 " --> pdb=" O GLY A 647 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 736 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.541A pdb=" N ARG A 821 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 843 " --> pdb=" O ARG A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.593A pdb=" N ILE A 919 " --> pdb=" O SER A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 947 removed outlier: 3.640A pdb=" N LEU A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 971 removed outlier: 3.800A pdb=" N PHE A 971 " --> pdb=" O ALA A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 997 Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.773A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1077 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1098 through 1106 Processing helix chain 'A' and resid 1121 through 1125 Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1144 through 1146 No H-bonds generated for 'chain 'A' and resid 1144 through 1146' Processing helix chain 'A' and resid 1258 through 1270 removed outlier: 4.134A pdb=" N LEU A1268 " --> pdb=" O GLU A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.687A pdb=" N VAL A1316 " --> pdb=" O ASN A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1327 Processing helix chain 'A' and resid 1331 through 1339 Processing helix chain 'A' and resid 1340 through 1358 Processing helix chain 'A' and resid 1364 through 1377 removed outlier: 3.893A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1400 Processing helix chain 'A' and resid 1405 through 1416 Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1453 Processing helix chain 'B' and resid 26 through 42 removed outlier: 3.517A pdb=" N SER B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 185 through 192 removed outlier: 3.711A pdb=" N TYR B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 307 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 326 through 339 Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 369 through 390 removed outlier: 3.563A pdb=" N LEU B 385 " --> pdb=" O MET B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 435 Processing helix chain 'B' and resid 443 through 464 removed outlier: 3.791A pdb=" N ALA B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.503A pdb=" N LEU B 492 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 529 through 533 removed outlier: 3.565A pdb=" N ALA B 532 " --> pdb=" O GLU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 671 Processing helix chain 'B' and resid 680 through 688 Processing helix chain 'B' and resid 695 through 699 removed outlier: 4.071A pdb=" N GLU B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 695 through 699' Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 711 through 716 Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.529A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 3.779A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 787 removed outlier: 4.594A pdb=" N ASN B 786 " --> pdb=" O THR B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 813 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1014 through 1017 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.858A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.523A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1121 through 1125 Processing helix chain 'B' and resid 1131 through 1142 removed outlier: 3.500A pdb=" N CYS B1137 " --> pdb=" O MET B1133 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET B1138 " --> pdb=" O GLU B1134 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B1140 " --> pdb=" O ASP B1136 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.879A pdb=" N ALA C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.682A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.735A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 134 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 169 removed outlier: 4.064A pdb=" N ALA D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL D 163 " --> pdb=" O THR D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 195 through 202 removed outlier: 3.570A pdb=" N ASN D 199 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN D 200 " --> pdb=" O PRO D 196 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 221 removed outlier: 3.669A pdb=" N TYR D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 26 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 138 through 142 removed outlier: 3.575A pdb=" N VAL E 142 " --> pdb=" O ALA E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 19 through 20 No H-bonds generated for 'chain 'G' and resid 19 through 20' Processing helix chain 'G' and resid 21 through 35 removed outlier: 4.038A pdb=" N LYS G 27 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.561A pdb=" N ASP H 86 " --> pdb=" O GLN H 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'I' and resid 116 through 122 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 4.608A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 39 through 51 removed outlier: 4.312A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 117 removed outlier: 3.865A pdb=" N ALA K 115 " --> pdb=" O LEU K 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 299 through 315 Processing helix chain 'M' and resid 328 through 340 removed outlier: 3.555A pdb=" N UNK M 333 " --> pdb=" O UNK M 329 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N UNK M 338 " --> pdb=" O UNK M 334 " (cutoff:3.500A) Processing helix chain 'M' and resid 354 through 369 removed outlier: 5.114A pdb=" N UNK M 360 " --> pdb=" O UNK M 356 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N UNK M 363 " --> pdb=" O UNK M 359 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N UNK M 366 " --> pdb=" O UNK M 362 " (cutoff:3.500A) Processing helix chain 'M' and resid 380 through 386 removed outlier: 3.702A pdb=" N UNK M 386 " --> pdb=" O UNK M 382 " (cutoff:3.500A) Processing helix chain 'M' and resid 447 through 455 Processing helix chain 'M' and resid 470 through 474 Processing helix chain 'M' and resid 479 through 488 Processing helix chain 'M' and resid 504 through 512 removed outlier: 4.021A pdb=" N UNK M 510 " --> pdb=" O UNK M 506 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N UNK M 511 " --> pdb=" O UNK M 507 " (cutoff:3.500A) Processing helix chain 'M' and resid 522 through 530 removed outlier: 3.597A pdb=" N UNK M 528 " --> pdb=" O UNK M 524 " (cutoff:3.500A) Processing helix chain 'M' and resid 530 through 537 Processing helix chain 'M' and resid 546 through 563 removed outlier: 3.655A pdb=" N UNK M 550 " --> pdb=" O UNK M 546 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N UNK M 563 " --> pdb=" O UNK M 559 " (cutoff:3.500A) Processing helix chain 'M' and resid 569 through 573 Processing helix chain 'M' and resid 590 through 602 Processing helix chain 'M' and resid 605 through 609 Processing helix chain 'M' and resid 613 through 629 removed outlier: 3.634A pdb=" N UNK M 627 " --> pdb=" O UNK M 623 " (cutoff:3.500A) Processing helix chain 'M' and resid 646 through 649 Processing helix chain 'M' and resid 650 through 666 Processing helix chain 'M' and resid 676 through 689 Processing helix chain 'M' and resid 691 through 696 removed outlier: 4.026A pdb=" N UNK M 695 " --> pdb=" O UNK M 691 " (cutoff:3.500A) Processing helix chain 'M' and resid 707 through 720 Processing helix chain 'M' and resid 729 through 734 Processing helix chain 'M' and resid 753 through 765 removed outlier: 4.209A pdb=" N UNK M 759 " --> pdb=" O UNK M 755 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N UNK M 760 " --> pdb=" O UNK M 756 " (cutoff:3.500A) Processing helix chain 'M' and resid 783 through 797 removed outlier: 3.506A pdb=" N UNK M 787 " --> pdb=" O UNK M 783 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N UNK M 797 " --> pdb=" O UNK M 793 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 34 removed outlier: 6.680A pdb=" N ALA A 33 " --> pdb=" O HIS A 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 91 removed outlier: 10.724A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.510A pdb=" N LYS A 343 " --> pdb=" O PHE B1130 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.640A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER A 354 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 375 through 379 removed outlier: 4.251A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AB1, first strand: chain 'A' and resid 587 through 590 removed outlier: 6.899A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 849 through 850 removed outlier: 3.852A pdb=" N ARG A 857 " --> pdb=" O MET A 849 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB4, first strand: chain 'A' and resid 1282 through 1292 Processing sheet with id=AB5, first strand: chain 'A' and resid 1141 through 1142 Processing sheet with id=AB6, first strand: chain 'A' and resid 1149 through 1152 removed outlier: 3.705A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 143 through 147 removed outlier: 4.810A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 143 through 147 removed outlier: 4.810A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 68 through 71 removed outlier: 4.944A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER B 126 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG B 169 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU B 128 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC2, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.508A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 222 through 227 removed outlier: 3.603A pdb=" N ILE B 222 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG B 241 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 544 through 545 removed outlier: 3.657A pdb=" N ILE B 693 " --> pdb=" O ARG B 635 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC6, first strand: chain 'B' and resid 564 through 565 removed outlier: 3.622A pdb=" N HIS B 587 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL B 580 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL B 589 " --> pdb=" O THR B 578 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR B 578 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE B 627 " --> pdb=" O SER B 614 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 793 through 796 removed outlier: 6.218A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 3.507A pdb=" N ILE B1085 " --> pdb=" O GLU B1070 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 981 " --> pdb=" O GLN B1093 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B1012 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD1, first strand: chain 'B' and resid 1157 through 1163 removed outlier: 3.603A pdb=" N PHE B1158 " --> pdb=" O ILE B1196 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B1192 " --> pdb=" O ILE B1162 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1172 through 1173 Processing sheet with id=AD3, first strand: chain 'C' and resid 7 through 13 removed outlier: 7.033A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.850A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.755A pdb=" N GLN C 73 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AD7, first strand: chain 'E' and resid 60 through 62 removed outlier: 5.643A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLY E 108 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE E 135 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE E 110 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AD9, first strand: chain 'G' and resid 142 through 146 removed outlier: 6.292A pdb=" N VAL G 91 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN G 102 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 95 through 98 removed outlier: 3.738A pdb=" N THR H 56 " --> pdb=" O ARG H 145 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE H 6 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU H 14 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS H 37 " --> pdb=" O GLU H 126 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 16 through 19 Processing sheet with id=AE3, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.561A pdb=" N SER I 71 " --> pdb=" O ASN I 83 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE5, first strand: chain 'M' and resid 374 through 376 removed outlier: 6.681A pdb=" N UNK M 375 " --> pdb=" O UNK M 445 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N UNK M 351 " --> pdb=" O UNK M 446 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N UNK M 350 " --> pdb=" O UNK M 467 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N UNK M 466 " --> pdb=" O UNK M 494 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N UNK M 496 " --> pdb=" O UNK M 466 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N UNK M 468 " --> pdb=" O UNK M 496 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N UNK M 495 " --> pdb=" O UNK M 318 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N UNK M 319 " --> pdb=" O UNK M 566 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 582 through 587 removed outlier: 7.339A pdb=" N UNK M 583 " --> pdb=" O UNK M 777 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N UNK M 779 " --> pdb=" O UNK M 583 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N UNK M 585 " --> pdb=" O UNK M 779 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N UNK M 745 " --> pdb=" O UNK M 776 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N UNK M 778 " --> pdb=" O UNK M 745 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N UNK M 747 " --> pdb=" O UNK M 778 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N UNK M 780 " --> pdb=" O UNK M 747 " (cutoff:3.500A) removed outlier: 12.078A pdb=" N UNK M 749 " --> pdb=" O UNK M 780 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N UNK M 671 " --> pdb=" O UNK M 746 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N UNK M 748 " --> pdb=" O UNK M 671 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N UNK M 673 " --> pdb=" O UNK M 748 " (cutoff:3.500A) 1447 hydrogen bonds defined for protein. 3987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 77 stacking parallelities Total time for adding SS restraints: 25.96 Time building geometry restraints manager: 15.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 24924 1.03 - 1.23: 84 1.23 - 1.42: 13361 1.42 - 1.62: 18955 1.62 - 1.81: 274 Bond restraints: 57598 Sorted by residual: bond pdb=" C1' DG N 7 " pdb=" N9 DG N 7 " ideal model delta sigma weight residual 1.460 1.388 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C1' DG T 7 " pdb=" N9 DG T 7 " ideal model delta sigma weight residual 1.460 1.392 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C1' DA N 3 " pdb=" N9 DA N 3 " ideal model delta sigma weight residual 1.460 1.393 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C1' DA N 42 " pdb=" N9 DA N 42 " ideal model delta sigma weight residual 1.460 1.396 0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C1' DA T 43 " pdb=" N9 DA T 43 " ideal model delta sigma weight residual 1.460 1.398 0.062 2.00e-02 2.50e+03 9.62e+00 ... (remaining 57593 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 100079 2.03 - 4.05: 1409 4.05 - 6.08: 89 6.08 - 8.11: 25 8.11 - 10.13: 5 Bond angle restraints: 101607 Sorted by residual: angle pdb=" N PRO G 116 " pdb=" CA PRO G 116 " pdb=" CB PRO G 116 " ideal model delta sigma weight residual 103.25 111.09 -7.84 8.80e-01 1.29e+00 7.95e+01 angle pdb=" N PRO B 293 " pdb=" CA PRO B 293 " pdb=" CB PRO B 293 " ideal model delta sigma weight residual 103.17 111.09 -7.92 8.90e-01 1.26e+00 7.93e+01 angle pdb=" N PRO A 321 " pdb=" CA PRO A 321 " pdb=" CB PRO A 321 " ideal model delta sigma weight residual 103.31 111.11 -7.80 8.90e-01 1.26e+00 7.68e+01 angle pdb=" N PRO B 281 " pdb=" CA PRO B 281 " pdb=" CB PRO B 281 " ideal model delta sigma weight residual 103.31 111.10 -7.79 8.90e-01 1.26e+00 7.66e+01 angle pdb=" N PRO A 978 " pdb=" CA PRO A 978 " pdb=" CB PRO A 978 " ideal model delta sigma weight residual 103.33 111.12 -7.79 9.30e-01 1.16e+00 7.01e+01 ... (remaining 101602 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.77: 26633 34.77 - 69.55: 903 69.55 - 104.32: 39 104.32 - 139.10: 1 139.10 - 173.87: 2 Dihedral angle restraints: 27578 sinusoidal: 14229 harmonic: 13349 Sorted by residual: dihedral pdb=" O4' A R 10 " pdb=" C2' A R 10 " pdb=" C1' A R 10 " pdb=" C3' A R 10 " ideal model delta sinusoidal sigma weight residual 25.00 -18.19 43.19 1 8.00e+00 1.56e-02 4.06e+01 dihedral pdb=" O4' C R 13 " pdb=" C1' C R 13 " pdb=" N1 C R 13 " pdb=" C2 C R 13 " ideal model delta sinusoidal sigma weight residual -160.00 -83.07 -76.93 1 1.50e+01 4.44e-03 3.30e+01 dihedral pdb=" C4' A R 10 " pdb=" O4' A R 10 " pdb=" C1' A R 10 " pdb=" C2' A R 10 " ideal model delta sinusoidal sigma weight residual 3.00 -33.45 36.45 1 8.00e+00 1.56e-02 2.93e+01 ... (remaining 27575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 4735 0.086 - 0.171: 460 0.171 - 0.257: 38 0.257 - 0.342: 0 0.342 - 0.428: 1 Chirality restraints: 5234 Sorted by residual: chirality pdb=" C3' DT T 29 " pdb=" C4' DT T 29 " pdb=" O3' DT T 29 " pdb=" C2' DT T 29 " both_signs ideal model delta sigma weight residual False -2.66 -2.23 -0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" C2' C R 3 " pdb=" C3' C R 3 " pdb=" O2' C R 3 " pdb=" C1' C R 3 " both_signs ideal model delta sigma weight residual False -2.75 -2.51 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C3' DT N 21 " pdb=" C4' DT N 21 " pdb=" O3' DT N 21 " pdb=" C2' DT N 21 " both_signs ideal model delta sigma weight residual False -2.66 -2.42 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 5231 not shown) Planarity restraints: 8491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 66 " 0.273 9.50e-02 1.11e+02 9.16e-02 1.12e+01 pdb=" NE ARG D 66 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG D 66 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 66 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 66 " 0.022 2.00e-02 2.50e+03 pdb="HH11 ARG D 66 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG D 66 " -0.005 2.00e-02 2.50e+03 pdb="HH21 ARG D 66 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG D 66 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 463 " -0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO A 464 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 464 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 464 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC T 22 " -0.024 2.00e-02 2.50e+03 1.31e-02 3.84e+00 pdb=" N1 DC T 22 " 0.029 2.00e-02 2.50e+03 pdb=" C2 DC T 22 " 0.003 2.00e-02 2.50e+03 pdb=" O2 DC T 22 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DC T 22 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DC T 22 " -0.006 2.00e-02 2.50e+03 pdb=" N4 DC T 22 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DC T 22 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC T 22 " 0.006 2.00e-02 2.50e+03 ... (remaining 8488 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.02: 830 2.02 - 2.67: 74418 2.67 - 3.31: 159894 3.31 - 3.96: 204877 3.96 - 4.60: 318824 Nonbonded interactions: 758843 Sorted by model distance: nonbonded pdb="HH12 ARG A 175 " pdb=" OP1 DA N 39 " model vdw 1.377 2.450 nonbonded pdb=" HB2 CYS A 70 " pdb="ZN ZN A1802 " model vdw 1.424 1.544 nonbonded pdb=" OE1 GLN B 776 " pdb=" HE2 HIS B1097 " model vdw 1.520 2.450 nonbonded pdb=" OE1 GLU C 61 " pdb=" H GLU C 61 " model vdw 1.538 2.450 nonbonded pdb=" OE1 GLU B1053 " pdb=" H GLU B1053 " model vdw 1.556 2.450 ... (remaining 758838 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 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: 0.860 Extract box with map and model: 1.810 Check model and map are aligned: 0.340 Set scattering table: 0.430 Process input model: 139.720 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 32627 Z= 0.213 Angle : 0.765 10.134 44722 Z= 0.467 Chirality : 0.049 0.428 5234 Planarity : 0.004 0.129 5519 Dihedral : 15.193 173.871 11778 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.45 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3639 helix: 0.31 (0.15), residues: 1229 sheet: -1.14 (0.21), residues: 559 loop : -0.57 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 31 HIS 0.009 0.001 HIS C 167 PHE 0.014 0.001 PHE E 110 TYR 0.010 0.001 TYR C 114 ARG 0.006 0.000 ARG H 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 3.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ILE cc_start: 0.9636 (mt) cc_final: 0.9417 (tt) REVERT: A 1063 MET cc_start: 0.8667 (mmm) cc_final: 0.8276 (mmm) REVERT: A 1267 MET cc_start: 0.8844 (tpt) cc_final: 0.8362 (tpp) REVERT: A 1284 MET cc_start: 0.8960 (mmm) cc_final: 0.8422 (mmt) REVERT: A 1285 MET cc_start: 0.8709 (mmp) cc_final: 0.8353 (tpp) REVERT: B 597 MET cc_start: 0.8567 (ttm) cc_final: 0.8274 (ttm) REVERT: B 662 MET cc_start: 0.8509 (tmm) cc_final: 0.8283 (tmm) REVERT: B 1098 MET cc_start: 0.8289 (mmm) cc_final: 0.7379 (mtt) REVERT: C 75 MET cc_start: 0.8221 (mmp) cc_final: 0.7894 (mmp) REVERT: E 93 MET cc_start: 0.9225 (mmp) cc_final: 0.8905 (mmm) REVERT: G 70 PHE cc_start: 0.8463 (m-80) cc_final: 0.8085 (m-80) REVERT: J 49 MET cc_start: 0.8235 (tpp) cc_final: 0.7161 (tpp) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.7306 time to fit residues: 219.1305 Evaluate side-chains 150 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 3.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 352 optimal weight: 4.9990 chunk 316 optimal weight: 40.0000 chunk 175 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 326 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 243 optimal weight: 7.9990 chunk 378 optimal weight: 50.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN A 736 ASN ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 32627 Z= 0.338 Angle : 0.602 9.542 44722 Z= 0.333 Chirality : 0.040 0.253 5234 Planarity : 0.005 0.056 5519 Dihedral : 16.035 177.779 5569 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.99 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 3639 helix: 0.42 (0.14), residues: 1277 sheet: -1.31 (0.21), residues: 557 loop : -0.67 (0.15), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 656 HIS 0.007 0.001 HIS A 851 PHE 0.027 0.002 PHE B 51 TYR 0.015 0.002 TYR B 488 ARG 0.013 0.001 ARG H 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 3.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.9437 (m-30) cc_final: 0.9186 (m-30) REVERT: A 234 MET cc_start: 0.9242 (ttm) cc_final: 0.9013 (ttm) REVERT: A 1013 ASP cc_start: 0.8639 (m-30) cc_final: 0.8058 (m-30) REVERT: A 1267 MET cc_start: 0.8686 (tpt) cc_final: 0.8241 (tpp) REVERT: B 444 MET cc_start: 0.6967 (pmm) cc_final: 0.6598 (pmm) REVERT: B 999 MET cc_start: 0.9334 (mtp) cc_final: 0.9075 (mtp) REVERT: C 37 MET cc_start: 0.8944 (mtp) cc_final: 0.8544 (mtm) REVERT: E 7 ARG cc_start: 0.8725 (ttt180) cc_final: 0.8420 (tpp-160) REVERT: E 93 MET cc_start: 0.9293 (mmp) cc_final: 0.8855 (mmm) REVERT: G 48 VAL cc_start: 0.8777 (t) cc_final: 0.8157 (t) REVERT: J 49 MET cc_start: 0.8365 (tpp) cc_final: 0.7357 (tpp) REVERT: K 95 ILE cc_start: 0.9525 (mt) cc_final: 0.9298 (tt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.7781 time to fit residues: 213.0651 Evaluate side-chains 150 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 3.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 210 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 315 optimal weight: 30.0000 chunk 257 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 379 optimal weight: 50.0000 chunk 409 optimal weight: 20.0000 chunk 337 optimal weight: 40.0000 chunk 376 optimal weight: 50.0000 chunk 129 optimal weight: 2.9990 chunk 304 optimal weight: 40.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN B 657 HIS B 843 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 32627 Z= 0.422 Angle : 0.635 6.518 44722 Z= 0.350 Chirality : 0.041 0.266 5234 Planarity : 0.005 0.065 5519 Dihedral : 16.322 176.093 5569 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.13 % Favored : 91.81 % Rotamer: Outliers : 0.04 % Allowed : 2.26 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.14), residues: 3639 helix: 0.11 (0.14), residues: 1284 sheet: -1.72 (0.21), residues: 537 loop : -1.13 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 656 HIS 0.007 0.002 HIS B 572 PHE 0.018 0.002 PHE B1001 TYR 0.063 0.002 TYR B 797 ARG 0.006 0.001 ARG A 821 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 3.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.9457 (m-30) cc_final: 0.9207 (m-30) REVERT: A 210 ILE cc_start: 0.9565 (mt) cc_final: 0.9324 (tp) REVERT: A 234 MET cc_start: 0.9239 (ttm) cc_final: 0.8996 (ttm) REVERT: A 708 MET cc_start: 0.7998 (mmp) cc_final: 0.7711 (mmm) REVERT: B 444 MET cc_start: 0.6887 (pmm) cc_final: 0.6598 (pmm) REVERT: B 542 MET cc_start: 0.8633 (mtp) cc_final: 0.8300 (mtp) REVERT: C 265 MET cc_start: 0.8977 (tmm) cc_final: 0.8623 (tmm) REVERT: E 93 MET cc_start: 0.9321 (mmp) cc_final: 0.8985 (mmm) REVERT: H 1 MET cc_start: 0.2902 (mmp) cc_final: 0.0619 (ptp) REVERT: J 49 MET cc_start: 0.8251 (tpp) cc_final: 0.7459 (tpp) outliers start: 1 outliers final: 1 residues processed: 164 average time/residue: 0.7189 time to fit residues: 192.5161 Evaluate side-chains 152 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 374 optimal weight: 60.0000 chunk 285 optimal weight: 7.9990 chunk 196 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 254 optimal weight: 0.9980 chunk 380 optimal weight: 50.0000 chunk 403 optimal weight: 50.0000 chunk 198 optimal weight: 0.9980 chunk 360 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 overall best weight: 3.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32627 Z= 0.276 Angle : 0.538 6.800 44722 Z= 0.296 Chirality : 0.039 0.245 5234 Planarity : 0.004 0.060 5519 Dihedral : 16.228 178.588 5569 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.27 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3639 helix: 0.55 (0.14), residues: 1293 sheet: -1.75 (0.21), residues: 541 loop : -0.95 (0.15), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 656 HIS 0.006 0.001 HIS B 400 PHE 0.013 0.001 PHE A 252 TYR 0.016 0.002 TYR B 797 ARG 0.007 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 3.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.9422 (m-30) cc_final: 0.9149 (m-30) REVERT: A 210 ILE cc_start: 0.9543 (mt) cc_final: 0.9299 (tp) REVERT: A 234 MET cc_start: 0.9262 (ttm) cc_final: 0.8987 (ttm) REVERT: A 708 MET cc_start: 0.8022 (mmp) cc_final: 0.7636 (mmm) REVERT: A 1258 HIS cc_start: 0.8152 (p90) cc_final: 0.7928 (p90) REVERT: B 444 MET cc_start: 0.6786 (pmm) cc_final: 0.6553 (pmm) REVERT: B 542 MET cc_start: 0.8564 (mtp) cc_final: 0.8166 (mtp) REVERT: B 1002 THR cc_start: 0.9064 (p) cc_final: 0.8479 (p) REVERT: B 1072 MET cc_start: 0.8268 (ttm) cc_final: 0.7797 (tpp) REVERT: C 265 MET cc_start: 0.8944 (tmm) cc_final: 0.8613 (tmm) REVERT: E 93 MET cc_start: 0.9295 (mmp) cc_final: 0.8885 (mmm) REVERT: J 49 MET cc_start: 0.8336 (tpp) cc_final: 0.7569 (tpp) REVERT: K 95 ILE cc_start: 0.9524 (mt) cc_final: 0.9266 (tt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.7152 time to fit residues: 195.5099 Evaluate side-chains 149 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 3.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 335 optimal weight: 50.0000 chunk 228 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 300 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 343 optimal weight: 7.9990 chunk 278 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 361 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 966 ASN ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 32627 Z= 0.298 Angle : 0.537 6.428 44722 Z= 0.296 Chirality : 0.039 0.262 5234 Planarity : 0.004 0.105 5519 Dihedral : 16.149 177.799 5569 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.09 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3639 helix: 0.70 (0.14), residues: 1293 sheet: -1.79 (0.20), residues: 547 loop : -0.99 (0.15), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 656 HIS 0.007 0.001 HIS B 400 PHE 0.015 0.001 PHE K 71 TYR 0.025 0.002 TYR B 833 ARG 0.006 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.8913 (m-10) cc_final: 0.8711 (m-10) REVERT: A 151 ASP cc_start: 0.9404 (m-30) cc_final: 0.9133 (m-30) REVERT: A 210 ILE cc_start: 0.9553 (mt) cc_final: 0.9320 (tp) REVERT: A 234 MET cc_start: 0.9300 (ttm) cc_final: 0.9043 (ttm) REVERT: A 304 MET cc_start: 0.8975 (mmm) cc_final: 0.8298 (mmt) REVERT: A 708 MET cc_start: 0.8048 (mmp) cc_final: 0.7730 (mmm) REVERT: A 1258 HIS cc_start: 0.8174 (p90) cc_final: 0.7958 (p90) REVERT: B 542 MET cc_start: 0.8551 (mtp) cc_final: 0.8075 (mtp) REVERT: B 1002 THR cc_start: 0.9137 (p) cc_final: 0.8513 (p) REVERT: B 1072 MET cc_start: 0.8232 (ttm) cc_final: 0.7712 (tpp) REVERT: C 265 MET cc_start: 0.8963 (tmm) cc_final: 0.8640 (tmm) REVERT: E 93 MET cc_start: 0.9305 (mmp) cc_final: 0.8878 (mmm) REVERT: J 49 MET cc_start: 0.8295 (tpp) cc_final: 0.7457 (tpp) REVERT: K 95 ILE cc_start: 0.9515 (mt) cc_final: 0.9253 (tt) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.7255 time to fit residues: 197.0884 Evaluate side-chains 150 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 3.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 135 optimal weight: 1.9990 chunk 362 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 236 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 403 optimal weight: 50.0000 chunk 334 optimal weight: 40.0000 chunk 186 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32627 Z= 0.226 Angle : 0.496 5.519 44722 Z= 0.272 Chirality : 0.039 0.265 5234 Planarity : 0.004 0.064 5519 Dihedral : 16.053 179.203 5569 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.07 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3639 helix: 1.02 (0.15), residues: 1287 sheet: -1.72 (0.20), residues: 575 loop : -0.84 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 656 HIS 0.006 0.001 HIS C 167 PHE 0.015 0.001 PHE A 662 TYR 0.014 0.001 TYR K 61 ARG 0.010 0.000 ARG K 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 3.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.9383 (m-30) cc_final: 0.9104 (m-30) REVERT: A 210 ILE cc_start: 0.9540 (mt) cc_final: 0.9313 (tp) REVERT: A 234 MET cc_start: 0.9281 (ttm) cc_final: 0.9012 (ttm) REVERT: A 304 MET cc_start: 0.8942 (mmm) cc_final: 0.8213 (mmt) REVERT: A 708 MET cc_start: 0.8046 (mmp) cc_final: 0.7723 (mmm) REVERT: A 1258 HIS cc_start: 0.8203 (p90) cc_final: 0.7959 (p90) REVERT: B 542 MET cc_start: 0.8562 (mtp) cc_final: 0.8031 (mtp) REVERT: B 1002 THR cc_start: 0.9093 (p) cc_final: 0.8473 (p) REVERT: B 1072 MET cc_start: 0.8248 (ttm) cc_final: 0.7803 (tpp) REVERT: C 265 MET cc_start: 0.8974 (tmm) cc_final: 0.8726 (tmm) REVERT: E 93 MET cc_start: 0.9299 (mmp) cc_final: 0.8862 (mmm) REVERT: J 49 MET cc_start: 0.8294 (tpp) cc_final: 0.7618 (tpp) REVERT: K 95 ILE cc_start: 0.9543 (mt) cc_final: 0.9263 (tt) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.7213 time to fit residues: 193.9485 Evaluate side-chains 149 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 388 optimal weight: 50.0000 chunk 45 optimal weight: 1.9990 chunk 229 optimal weight: 4.9990 chunk 294 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 chunk 339 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 401 optimal weight: 50.0000 chunk 251 optimal weight: 5.9990 chunk 245 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32627 Z= 0.279 Angle : 0.520 8.237 44722 Z= 0.285 Chirality : 0.038 0.274 5234 Planarity : 0.004 0.060 5519 Dihedral : 16.012 177.954 5569 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.95 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3639 helix: 0.99 (0.15), residues: 1292 sheet: -1.80 (0.20), residues: 564 loop : -0.92 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 656 HIS 0.005 0.001 HIS A 851 PHE 0.017 0.001 PHE K 71 TYR 0.017 0.002 TYR B 833 ARG 0.005 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 3.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.9392 (m-30) cc_final: 0.9111 (m-30) REVERT: A 210 ILE cc_start: 0.9531 (mt) cc_final: 0.9298 (tp) REVERT: A 234 MET cc_start: 0.9301 (ttm) cc_final: 0.9039 (ttm) REVERT: A 304 MET cc_start: 0.9033 (mmm) cc_final: 0.8343 (mmt) REVERT: A 708 MET cc_start: 0.8131 (mmp) cc_final: 0.7778 (mmm) REVERT: A 1258 HIS cc_start: 0.8171 (p90) cc_final: 0.7944 (p90) REVERT: B 542 MET cc_start: 0.8608 (mtp) cc_final: 0.8072 (mtp) REVERT: B 1002 THR cc_start: 0.9094 (p) cc_final: 0.8412 (p) REVERT: B 1072 MET cc_start: 0.8228 (ttm) cc_final: 0.7705 (tpp) REVERT: C 265 MET cc_start: 0.8986 (tmm) cc_final: 0.8750 (tmm) REVERT: E 1 MET cc_start: 0.5352 (mtm) cc_final: 0.5124 (mtm) REVERT: E 93 MET cc_start: 0.9303 (mmp) cc_final: 0.8897 (mmm) REVERT: J 49 MET cc_start: 0.8298 (tpp) cc_final: 0.7482 (tpp) REVERT: K 95 ILE cc_start: 0.9525 (mt) cc_final: 0.9261 (tt) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.6779 time to fit residues: 182.0014 Evaluate side-chains 143 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.5264 > 50: distance: 44 - 47: 11.605 distance: 47 - 48: 14.985 distance: 48 - 49: 31.328 distance: 48 - 51: 16.264 distance: 49 - 50: 11.761 distance: 49 - 52: 47.104 distance: 52 - 53: 40.232 distance: 53 - 54: 22.371 distance: 53 - 56: 29.057 distance: 54 - 55: 19.412 distance: 54 - 57: 22.683 distance: 57 - 58: 9.060 distance: 58 - 59: 9.192 distance: 58 - 61: 11.467 distance: 59 - 60: 10.401 distance: 59 - 62: 13.808 distance: 62 - 63: 18.268 distance: 63 - 64: 18.195 distance: 63 - 66: 17.371 distance: 64 - 65: 22.861 distance: 64 - 67: 24.890 distance: 67 - 68: 18.963 distance: 68 - 69: 47.098 distance: 68 - 71: 18.176 distance: 69 - 70: 49.404 distance: 69 - 72: 59.526 distance: 72 - 73: 17.934 distance: 73 - 74: 26.872 distance: 73 - 76: 26.411 distance: 74 - 75: 26.196 distance: 74 - 77: 24.930 distance: 77 - 78: 33.942 distance: 78 - 79: 20.675 distance: 78 - 81: 12.340 distance: 79 - 80: 14.103 distance: 79 - 82: 26.187 distance: 82 - 83: 9.582 distance: 83 - 84: 38.221 distance: 83 - 86: 34.902 distance: 84 - 85: 32.922 distance: 84 - 87: 26.792 distance: 87 - 88: 18.837 distance: 88 - 89: 20.796 distance: 88 - 91: 14.787 distance: 89 - 90: 34.395 distance: 89 - 92: 32.884 distance: 92 - 93: 9.950 distance: 93 - 94: 15.890 distance: 94 - 95: 24.125 distance: 94 - 96: 16.460 distance: 95 - 111: 8.676