Starting phenix.real_space_refine on Wed Dec 13 18:04:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ok0_12960/12_2023/7ok0_12960_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ok0_12960/12_2023/7ok0_12960.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/7ok0_12960/12_2023/7ok0_12960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ok0_12960/12_2023/7ok0_12960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ok0_12960/12_2023/7ok0_12960_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ok0_12960/12_2023/7ok0_12960_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= -0.000 sd= 1.000 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 Fe 3 7.16 5 Zn 6 6.06 5 Mg 1 5.21 5 S 122 5.16 5 C 16294 2.51 5 N 4427 2.21 5 O 4783 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "A TYR 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 673": "OD1" <-> "OD2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "B ASP 30": "OD1" <-> "OD2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 759": "OE1" <-> "OE2" Residue "B GLU 841": "OE1" <-> "OE2" Residue "B ASP 846": "OD1" <-> "OD2" Residue "B ASP 998": "OD1" <-> "OD2" Residue "B ASP 1033": "OD1" <-> "OD2" Residue "B TYR 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D ASP 113": "OD1" <-> "OD2" Residue "E ASP 23": "OD1" <-> "OD2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G ASP 49": "OD1" <-> "OD2" Residue "G GLU 59": "OE1" <-> "OE2" Residue "G ASP 67": "OD1" <-> "OD2" Residue "G TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 43": "OD1" <-> "OD2" Residue "K ASP 51": "OD1" <-> "OD2" Residue "K GLU 57": "OE1" <-> "OE2" Residue "K GLU 58": "OE1" <-> "OE2" Residue "L GLU 14": "OE1" <-> "OE2" Residue "L ASP 18": "OD1" <-> "OD2" Residue "P ASP 14": "OD1" <-> "OD2" Residue "P ASP 15": "OD1" <-> "OD2" Residue "Q ASP 49": "OD1" <-> "OD2" Residue "Q GLU 51": "OE1" <-> "OE2" Residue "Q ASP 54": "OD1" <-> "OD2" Residue "Q TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 25636 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 880, 7023 Classifications: {'peptide': 880} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 48, 'TRANS': 827} 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: "B" Number of atoms: 8725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8725 Classifications: {'peptide': 1109} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1055} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 3087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3087 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 384} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2057 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 246} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 402 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "G" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 991 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 617 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 690 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "L" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 707 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain: "N" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 534 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "P" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 376 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 43} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Q" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 357 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 43} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'F3S': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" 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 435 SG CYS A 58 18.367 75.532 45.318 1.00124.98 S ATOM 455 SG CYS A 61 18.421 71.740 44.766 1.00122.81 S ATOM 497 SG CYS A 68 20.583 73.306 47.472 1.00117.60 S ATOM 744 SG CYS A 98 54.448 82.125 12.433 1.00133.82 S ATOM 775 SG CYS A 101 52.641 79.333 10.773 1.00135.01 S ATOM 1162 SG CYS A 146 56.435 79.218 10.850 1.00135.96 S ATOM 1185 SG CYS A 149 54.749 81.813 8.683 1.00138.63 S ATOM 4568 SG CYS A 575 83.314 38.808 91.778 1.00101.43 S ATOM 4608 SG CYS A 580 81.407 37.971 92.061 1.00 95.71 S ATOM 15263 SG CYS B1060 26.489 62.648 33.979 1.00106.21 S ATOM 15286 SG CYS B1063 28.705 65.672 34.066 1.00104.50 S ATOM 15417 SG CYS B1078 24.964 66.062 34.528 1.00114.57 S ATOM 20467 SG CYS D 209 72.142 53.258 122.116 1.00 73.26 S ATOM 20421 SG CYS D 203 66.228 53.698 123.074 1.00 61.07 S ATOM 20443 SG CYS D 206 67.977 56.107 119.534 1.00 62.13 S ATOM 20268 SG CYS D 183 68.476 58.536 124.159 1.00 67.39 S ATOM 24411 SG CYS N 7 49.304 70.647 113.304 1.00 45.72 S ATOM 24435 SG CYS N 10 48.935 67.656 115.689 1.00 49.44 S ATOM 24698 SG CYS N 44 52.354 68.655 114.415 1.00 48.19 S ATOM 24704 SG CYS N 45 50.547 70.803 116.958 1.00 48.07 S ATOM 24932 SG CYS P 6 26.195 105.880 98.468 1.00 96.89 S ATOM 25082 SG CYS P 26 23.396 107.491 97.973 1.00103.51 S ATOM 25107 SG CYS P 29 26.386 108.729 98.722 1.00109.19 S Time building chain proxies: 13.44, per 1000 atoms: 0.52 Number of scatterers: 25636 At special positions: 0 Unit cell: (126.945, 149.73, 149.73, 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 6 29.99 Fe 3 26.01 S 122 16.00 Mg 1 11.99 O 4783 8.00 N 4427 7.00 C 16294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS G 9 " - pdb=" SG CYS G 29 " distance=2.04 Simple disulfide: pdb=" SG CYS G 69 " - pdb=" SG CYS G 119 " distance=2.05 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: 9.96 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S D 301 " pdb="FE4 F3S D 301 " - pdb=" SG CYS D 183 " pdb="FE1 F3S D 301 " - pdb=" SG CYS D 209 " pdb="FE3 F3S D 301 " - pdb=" SG CYS D 203 " pdb="FE3 F3S D 301 " - pdb=" SG CYS D 206 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 71 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 61 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 68 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 58 " pdb=" ZN A 903 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 98 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 101 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 146 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 149 " pdb=" ZN A 904 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 580 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 575 " pdb="ZN ZN A 904 " - pdb=" ND1 HIS A 582 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" ND1 HIS B1081 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1063 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1060 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1078 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 10 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 44 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 45 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 7 " pdb=" ZN P 101 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 29 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 6 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 26 " Number of angles added : 18 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6018 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 119 helices and 33 sheets defined 34.8% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.93 Creating SS restraints... Processing helix chain 'A' and resid 16 through 22 Processing helix chain 'A' and resid 84 through 92 removed outlier: 3.704A pdb=" N VAL A 87 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LYS A 88 " --> pdb=" O GLY A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 121 Processing helix chain 'A' and resid 126 through 141 Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.862A pdb=" N ARG A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 192 No H-bonds generated for 'chain 'A' and resid 189 through 192' Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 234 through 255 Processing helix chain 'A' and resid 259 through 277 Processing helix chain 'A' and resid 298 through 301 No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 341 through 346 Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 394 through 400 removed outlier: 3.710A pdb=" N SER A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 447 through 453 removed outlier: 3.722A pdb=" N CYS A 450 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Proline residue: A 451 - end of helix No H-bonds generated for 'chain 'A' and resid 447 through 453' Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 518 through 527 removed outlier: 4.321A pdb=" N VAL A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 554 removed outlier: 3.572A pdb=" N LEU A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 603 No H-bonds generated for 'chain 'A' and resid 600 through 603' Processing helix chain 'A' and resid 611 through 641 removed outlier: 7.037A pdb=" N THR A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N GLU A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE A 632 " --> pdb=" O MET A 628 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N MET A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A 635 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 636 " --> pdb=" O PHE A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 655 through 681 removed outlier: 3.609A pdb=" N GLU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU A 681 " --> pdb=" O ARG A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 717 Processing helix chain 'A' and resid 724 through 731 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 776 through 779 No H-bonds generated for 'chain 'A' and resid 776 through 779' Processing helix chain 'A' and resid 792 through 826 removed outlier: 4.985A pdb=" N GLU A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLY A 805 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 806 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 807 " --> pdb=" O ARG A 803 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR A 809 " --> pdb=" O GLY A 805 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ALA A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL A 811 " --> pdb=" O VAL A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 879 removed outlier: 6.418A pdb=" N TRP A 878 " --> pdb=" O ARG A 874 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS A 879 " --> pdb=" O VAL A 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 17 Processing helix chain 'B' and resid 22 through 33 Processing helix chain 'B' and resid 35 through 43 removed outlier: 3.912A pdb=" N ILE B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 127 through 130 removed outlier: 3.901A pdb=" N ASN B 130 " --> pdb=" O PRO B 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 127 through 130' Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 233 through 240 Processing helix chain 'B' and resid 244 through 257 removed outlier: 3.935A pdb=" N GLU B 249 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Proline residue: B 252 - end of helix removed outlier: 3.732A pdb=" N ALA B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 274 Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 325 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 344 through 373 Processing helix chain 'B' and resid 379 through 382 Processing helix chain 'B' and resid 385 through 396 removed outlier: 3.949A pdb=" N THR B 389 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE B 392 " --> pdb=" O THR B 389 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG B 393 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N HIS B 394 " --> pdb=" O ARG B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 417 through 425 removed outlier: 3.677A pdb=" N ARG B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 480 through 490 Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 510 through 514 removed outlier: 3.873A pdb=" N SER B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 510 through 514' Processing helix chain 'B' and resid 531 through 543 Processing helix chain 'B' and resid 589 through 595 Processing helix chain 'B' and resid 602 through 607 Processing helix chain 'B' and resid 616 through 621 removed outlier: 3.616A pdb=" N GLU B 620 " --> pdb=" O ALA B 616 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASN B 621 " --> pdb=" O GLU B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 621' Processing helix chain 'B' and resid 628 through 630 No H-bonds generated for 'chain 'B' and resid 628 through 630' Processing helix chain 'B' and resid 642 through 645 removed outlier: 3.931A pdb=" N ILE B 645 " --> pdb=" O PRO B 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 642 through 645' Processing helix chain 'B' and resid 650 through 652 No H-bonds generated for 'chain 'B' and resid 650 through 652' Processing helix chain 'B' and resid 656 through 658 No H-bonds generated for 'chain 'B' and resid 656 through 658' Processing helix chain 'B' and resid 661 through 673 removed outlier: 3.675A pdb=" N THR B 665 " --> pdb=" O SER B 661 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN B 673 " --> pdb=" O ALA B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 708 removed outlier: 4.056A pdb=" N VAL B 708 " --> pdb=" O ARG B 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 704 through 708' Processing helix chain 'B' and resid 740 through 744 Processing helix chain 'B' and resid 786 through 788 No H-bonds generated for 'chain 'B' and resid 786 through 788' Processing helix chain 'B' and resid 910 through 916 Proline residue: B 914 - end of helix Processing helix chain 'B' and resid 919 through 934 Processing helix chain 'B' and resid 949 through 959 Processing helix chain 'B' and resid 996 through 998 No H-bonds generated for 'chain 'B' and resid 996 through 998' Processing helix chain 'B' and resid 1029 through 1038 Processing helix chain 'B' and resid 1041 through 1048 Processing helix chain 'B' and resid 1094 through 1105 Processing helix chain 'C' and resid 4 through 17 removed outlier: 3.879A pdb=" N GLU C 16 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 35 Processing helix chain 'C' and resid 43 through 59 Processing helix chain 'C' and resid 68 through 82 Proline residue: C 79 - end of helix removed outlier: 4.248A pdb=" N GLN C 82 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 126 through 128 No H-bonds generated for 'chain 'C' and resid 126 through 128' Processing helix chain 'C' and resid 132 through 142 removed outlier: 3.604A pdb=" N ILE C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 149 No H-bonds generated for 'chain 'C' and resid 147 through 149' Processing helix chain 'C' and resid 169 through 175 Processing helix chain 'C' and resid 179 through 189 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 267 through 269 No H-bonds generated for 'chain 'C' and resid 267 through 269' Processing helix chain 'C' and resid 275 through 281 Processing helix chain 'C' and resid 284 through 301 Processing helix chain 'C' and resid 308 through 318 Processing helix chain 'C' and resid 339 through 345 Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 380 through 383 Processing helix chain 'D' and resid 22 through 34 removed outlier: 3.836A pdb=" N ILE D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 63 Processing helix chain 'D' and resid 111 through 113 No H-bonds generated for 'chain 'D' and resid 111 through 113' Processing helix chain 'D' and resid 154 through 156 No H-bonds generated for 'chain 'D' and resid 154 through 156' Processing helix chain 'D' and resid 179 through 181 No H-bonds generated for 'chain 'D' and resid 179 through 181' Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'D' and resid 209 through 212 No H-bonds generated for 'chain 'D' and resid 209 through 212' Processing helix chain 'D' and resid 238 through 261 Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 22 through 33 removed outlier: 3.950A pdb=" N GLU E 33 " --> pdb=" O ILE E 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 41 through 43 No H-bonds generated for 'chain 'G' and resid 41 through 43' Processing helix chain 'H' and resid 25 through 35 Processing helix chain 'H' and resid 39 through 41 No H-bonds generated for 'chain 'H' and resid 39 through 41' Processing helix chain 'H' and resid 50 through 54 Processing helix chain 'K' and resid 5 through 16 removed outlier: 4.653A pdb=" N ASN K 16 " --> pdb=" O GLU K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 34 Processing helix chain 'K' and resid 52 through 62 Processing helix chain 'L' and resid 22 through 34 removed outlier: 3.890A pdb=" N LEU L 27 " --> pdb=" O THR L 23 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS L 34 " --> pdb=" O GLY L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 89 removed outlier: 3.973A pdb=" N LYS L 89 " --> pdb=" O ASP L 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 26 removed outlier: 3.545A pdb=" N TRP N 18 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLU N 19 " --> pdb=" O ASP N 16 " (cutoff:3.500A) Proline residue: N 20 - end of helix removed outlier: 3.697A pdb=" N ARG N 24 " --> pdb=" O PHE N 21 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL N 25 " --> pdb=" O SER N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 38 Processing helix chain 'N' and resid 43 through 50 Processing helix chain 'N' and resid 56 through 61 removed outlier: 5.014A pdb=" N HIS N 61 " --> pdb=" O ARG N 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 57 Processing helix chain 'Q' and resid 63 through 78 Processing sheet with id= A, first strand: chain 'A' and resid 73 through 76 Processing sheet with id= B, first strand: chain 'A' and resid 156 through 159 removed outlier: 3.784A pdb=" N LYS A 157 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 165 " --> pdb=" O LYS A 157 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 321 through 325 Processing sheet with id= D, first strand: chain 'A' and resid 326 through 328 removed outlier: 6.132A pdb=" N PHE A 443 " --> pdb=" O SER A 327 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.945A pdb=" N TYR A 377 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N HIS A 410 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA A 375 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 562 through 565 removed outlier: 3.588A pdb=" N GLU A 595 " --> pdb=" O VAL A 587 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LYS A 589 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 830 through 832 Processing sheet with id= H, first strand: chain 'B' and resid 53 through 57 removed outlier: 3.913A pdb=" N GLY B 115 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 96 " --> pdb=" O TYR B 113 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N TYR B 113 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N MET B 98 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLU B 111 " --> pdb=" O MET B 98 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 60 through 62 Processing sheet with id= J, first strand: chain 'B' and resid 150 through 152 Processing sheet with id= K, first strand: chain 'B' and resid 339 through 342 removed outlier: 3.749A pdb=" N ALA B 161 " --> pdb=" O ARG B 426 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 170 through 174 removed outlier: 6.941A pdb=" N ARG B 202 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL B 184 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 200 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS B 186 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B 198 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR B 188 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL B 196 " --> pdb=" O THR B 188 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 552 through 557 Processing sheet with id= N, first strand: chain 'B' and resid 575 through 578 Processing sheet with id= O, first strand: chain 'B' and resid 689 through 693 removed outlier: 6.001A pdb=" N ARG B 865 " --> pdb=" O VAL B 845 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL B 845 " --> pdb=" O ARG B 865 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 906 through 908 removed outlier: 4.183A pdb=" N LEU B 983 " --> pdb=" O ILE B 724 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 876 through 878 Processing sheet with id= R, first strand: chain 'B' and resid 1054 through 1060 Processing sheet with id= S, first strand: chain 'B' and resid 1068 through 1070 removed outlier: 3.611A pdb=" N ASP B1070 " --> pdb=" O ARG B1075 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG B1075 " --> pdb=" O ASP B1070 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 516 through 520 removed outlier: 5.984A pdb=" N LEU B 520 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 736 through 739 removed outlier: 7.867A pdb=" N MET B 738 " --> pdb=" O GLY B 887 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU B 889 " --> pdb=" O MET B 738 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 120 through 123 Processing sheet with id= W, first strand: chain 'C' and resid 151 through 157 removed outlier: 7.318A pdb=" N GLN C 166 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL C 154 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR C 164 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL C 156 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER C 162 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER C 203 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N THR C 205 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP C 198 " --> pdb=" O THR C 205 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 3 through 8 removed outlier: 6.891A pdb=" N ARG D 14 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG D 8 " --> pdb=" O ARG D 12 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG D 12 " --> pdb=" O ARG D 8 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL D 161 " --> pdb=" O GLU D 231 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 94 through 101 removed outlier: 3.584A pdb=" N GLU D 43 " --> pdb=" O ARG D 144 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG D 146 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL D 41 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY D 148 " --> pdb=" O MET D 39 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N MET D 39 " --> pdb=" O GLY D 148 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 167 through 172 removed outlier: 4.754A pdb=" N TYR D 167 " --> pdb=" O VAL D 222 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 107 through 110 removed outlier: 3.645A pdb=" N VAL D 131 " --> pdb=" O ILE D 109 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 8 through 13 Processing sheet with id= AC, first strand: chain 'G' and resid 94 through 100 removed outlier: 3.892A pdb=" N LEU G 94 " --> pdb=" O LEU G 91 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU G 76 " --> pdb=" O GLU G 88 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N SER G 90 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU G 74 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP G 114 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS G 10 " --> pdb=" O ASP G 28 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS G 26 " --> pdb=" O SER G 12 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE G 14 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL G 24 " --> pdb=" O ILE G 14 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 19 through 22 Processing sheet with id= AE, first strand: chain 'K' and resid 68 through 72 Processing sheet with id= AF, first strand: chain 'L' and resid 2 through 8 removed outlier: 6.770A pdb=" N GLU L 14 " --> pdb=" O ILE L 6 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU L 8 " --> pdb=" O TYR L 12 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR L 12 " --> pdb=" O GLU L 8 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'P' and resid 14 through 16 859 hydrogen bonds defined for protein. 2463 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.83 Time building geometry restraints manager: 10.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.83: 26064 1.83 - 2.43: 8 2.43 - 3.03: 0 3.03 - 3.64: 0 3.64 - 4.24: 3 Bond restraints: 26075 Sorted by residual: bond pdb=" S4 F3S D 301 " pdb="FE1 F3S D 301 " ideal model delta sigma weight residual 2.233 4.243 -2.010 2.00e-02 2.50e+03 1.01e+04 bond pdb=" S1 F3S D 301 " pdb="FE4 F3S D 301 " ideal model delta sigma weight residual 2.258 4.230 -1.972 2.00e-02 2.50e+03 9.72e+03 bond pdb=" S2 F3S D 301 " pdb="FE3 F3S D 301 " ideal model delta sigma weight residual 2.300 4.187 -1.887 2.00e-02 2.50e+03 8.90e+03 bond pdb=" S2 F3S D 301 " pdb="FE4 F3S D 301 " ideal model delta sigma weight residual 2.317 2.202 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" S3 F3S D 301 " pdb="FE1 F3S D 301 " ideal model delta sigma weight residual 2.296 2.192 0.104 2.00e-02 2.50e+03 2.68e+01 ... (remaining 26070 not shown) Histogram of bond angle deviations from ideal: 39.39 - 61.54: 6 61.54 - 83.68: 6 83.68 - 105.82: 574 105.82 - 127.96: 34463 127.96 - 150.11: 158 Bond angle restraints: 35207 Sorted by residual: angle pdb=" S1 F3S D 301 " pdb="FE4 F3S D 301 " pdb=" S3 F3S D 301 " ideal model delta sigma weight residual 114.75 39.54 75.21 3.00e+00 1.11e-01 6.29e+02 angle pdb=" S3 F3S D 301 " pdb="FE1 F3S D 301 " pdb=" S4 F3S D 301 " ideal model delta sigma weight residual 112.59 39.39 73.20 3.00e+00 1.11e-01 5.95e+02 angle pdb=" S1 F3S D 301 " pdb="FE3 F3S D 301 " pdb=" S4 F3S D 301 " ideal model delta sigma weight residual 112.54 150.11 -37.57 3.00e+00 1.11e-01 1.57e+02 angle pdb="FE1 F3S D 301 " pdb=" S4 F3S D 301 " pdb="FE3 F3S D 301 " ideal model delta sigma weight residual 74.86 43.55 31.31 3.00e+00 1.11e-01 1.09e+02 angle pdb="FE3 F3S D 301 " pdb=" S1 F3S D 301 " pdb="FE4 F3S D 301 " ideal model delta sigma weight residual 73.06 43.65 29.41 3.00e+00 1.11e-01 9.61e+01 ... (remaining 35202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 14532 16.88 - 33.76: 1255 33.76 - 50.64: 223 50.64 - 67.52: 34 67.52 - 84.40: 17 Dihedral angle restraints: 16061 sinusoidal: 6697 harmonic: 9364 Sorted by residual: dihedral pdb=" CB CYS G 9 " pdb=" SG CYS G 9 " pdb=" SG CYS G 29 " pdb=" CB CYS G 29 " ideal model delta sinusoidal sigma weight residual 93.00 36.02 56.98 1 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" CB CYS G 69 " pdb=" SG CYS G 69 " pdb=" SG CYS G 119 " pdb=" CB CYS G 119 " ideal model delta sinusoidal sigma weight residual 93.00 48.23 44.77 1 1.00e+01 1.00e-02 2.78e+01 dihedral pdb=" CA SER B1072 " pdb=" C SER B1072 " pdb=" N LYS B1073 " pdb=" CA LYS B1073 " ideal model delta harmonic sigma weight residual 180.00 161.05 18.95 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 16058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 2.704: 3997 2.704 - 5.408: 0 5.408 - 8.111: 0 8.111 - 10.815: 0 10.815 - 13.519: 1 Chirality restraints: 3998 Sorted by residual: chirality pdb=" S2 F3S D 301 " pdb="FE1 F3S D 301 " pdb="FE3 F3S D 301 " pdb="FE4 F3S D 301 " both_signs ideal model delta sigma weight residual False 10.77 -2.75 13.52 2.00e-01 2.50e+01 4.57e+03 chirality pdb=" CA CYS G 69 " pdb=" N CYS G 69 " pdb=" C CYS G 69 " pdb=" CB CYS G 69 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE C 214 " pdb=" CA ILE C 214 " pdb=" CG1 ILE C 214 " pdb=" CG2 ILE C 214 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.33e-01 ... (remaining 3995 not shown) Planarity restraints: 4519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS P 39 " -0.036 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO P 40 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO P 40 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO P 40 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 38 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO A 39 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1069 " -0.013 2.00e-02 2.50e+03 1.21e-02 2.92e+00 pdb=" CG TYR B1069 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B1069 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B1069 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B1069 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B1069 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B1069 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B1069 " 0.004 2.00e-02 2.50e+03 ... (remaining 4516 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 227 2.61 - 3.18: 21666 3.18 - 3.76: 37307 3.76 - 4.33: 54702 4.33 - 4.90: 92368 Nonbonded interactions: 206270 Sorted by model distance: nonbonded pdb=" OD1 ASP A 456 " pdb="MG MG A 901 " model vdw 2.038 2.170 nonbonded pdb=" OD2 ASP A 460 " pdb="MG MG A 901 " model vdw 2.056 2.170 nonbonded pdb=" OD1 ASP A 460 " pdb="MG MG A 901 " model vdw 2.063 2.170 nonbonded pdb=" OG1 THR D 171 " pdb=" OG SER D 218 " model vdw 2.067 2.440 nonbonded pdb=" OD2 ASP A 458 " pdb="MG MG A 901 " model vdw 2.076 2.170 ... (remaining 206265 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 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: 0.010 Extract box with map and model: 9.240 Check model and map are aligned: 0.370 Set scattering table: 0.290 Process input model: 76.000 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:13.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 0.021 2.010 26075 Z= 1.295 Angle : 0.929 75.214 35207 Z= 0.379 Chirality : 0.218 13.519 3998 Planarity : 0.004 0.056 4519 Dihedral : 12.908 84.403 10037 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.12 (0.15), residues: 3202 helix: 1.05 (0.16), residues: 1140 sheet: 0.30 (0.24), residues: 481 loop : -0.68 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 8 HIS 0.007 0.001 HIS A 426 PHE 0.024 0.001 PHE A 419 TYR 0.029 0.001 TYR B1069 ARG 0.006 0.000 ARG C 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 3.226 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 1.5316 time to fit residues: 646.2617 Evaluate side-chains 279 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 2.243 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 162 optimal weight: 0.0060 chunk 128 optimal weight: 0.2980 chunk 249 optimal weight: 0.1980 chunk 96 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 288 optimal weight: 0.8980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 272 HIS ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1001 HIS B1009 GLN C 199 ASN C 326 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.170 26075 Z= 0.197 Angle : 0.865 79.855 35207 Z= 0.347 Chirality : 0.067 3.231 3998 Planarity : 0.004 0.048 4519 Dihedral : 3.796 20.274 3559 Min Nonbonded Distance : 1.543 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.42 % Allowed : 8.03 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.25 (0.15), residues: 3202 helix: 1.20 (0.16), residues: 1154 sheet: 0.37 (0.24), residues: 492 loop : -0.65 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 8 HIS 0.006 0.001 HIS B1001 PHE 0.018 0.001 PHE A 419 TYR 0.019 0.001 TYR A 818 ARG 0.010 0.000 ARG P 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 286 time to evaluate : 2.962 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 16 residues processed: 304 average time/residue: 1.6078 time to fit residues: 558.0615 Evaluate side-chains 288 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 272 time to evaluate : 2.948 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 9 residues processed: 8 average time/residue: 0.9227 time to fit residues: 13.1852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 240 optimal weight: 0.6980 chunk 196 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 289 optimal weight: 0.8980 chunk 312 optimal weight: 20.0000 chunk 257 optimal weight: 1.9990 chunk 286 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 232 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 272 HIS A 605 ASN ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 GLN C 97 ASN C 199 ASN C 326 GLN ** C 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 26075 Z= 0.319 Angle : 0.729 77.692 35207 Z= 0.322 Chirality : 0.054 1.862 3998 Planarity : 0.004 0.049 4519 Dihedral : 4.006 21.359 3559 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.63 % Allowed : 9.88 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.14 (0.15), residues: 3202 helix: 1.11 (0.16), residues: 1146 sheet: 0.35 (0.24), residues: 478 loop : -0.72 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 8 HIS 0.008 0.001 HIS A 426 PHE 0.016 0.001 PHE A 419 TYR 0.017 0.001 TYR B 336 ARG 0.014 0.000 ARG Q 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 286 time to evaluate : 3.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 22 residues processed: 305 average time/residue: 1.6363 time to fit residues: 569.2848 Evaluate side-chains 290 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 268 time to evaluate : 3.038 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 11 residues processed: 12 average time/residue: 0.5365 time to fit residues: 13.2382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 138 optimal weight: 0.1980 chunk 194 optimal weight: 4.9990 chunk 290 optimal weight: 3.9990 chunk 307 optimal weight: 0.8980 chunk 151 optimal weight: 0.0020 chunk 275 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 272 HIS A 683 GLN B1009 GLN C 97 ASN ** C 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 26075 Z= 0.211 Angle : 0.707 81.686 35207 Z= 0.307 Chirality : 0.050 1.534 3998 Planarity : 0.004 0.049 4519 Dihedral : 3.916 21.093 3559 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.78 % Allowed : 11.40 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.20 (0.15), residues: 3202 helix: 1.16 (0.16), residues: 1148 sheet: 0.35 (0.24), residues: 495 loop : -0.70 (0.16), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 8 HIS 0.007 0.001 HIS A 426 PHE 0.012 0.001 PHE A 419 TYR 0.020 0.001 TYR G 118 ARG 0.009 0.000 ARG Q 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 276 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 20 residues processed: 303 average time/residue: 1.5607 time to fit residues: 542.4636 Evaluate side-chains 299 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 279 time to evaluate : 3.104 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 12 residues processed: 8 average time/residue: 0.5255 time to fit residues: 10.1129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 0.5980 chunk 174 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 262 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 275 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 HIS A 683 GLN C 97 ASN G 6 GLN K 46 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 26075 Z= 0.261 Angle : 0.721 81.423 35207 Z= 0.315 Chirality : 0.051 1.572 3998 Planarity : 0.004 0.050 4519 Dihedral : 3.990 21.673 3559 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.85 % Rotamer: Outliers : 1.92 % Allowed : 12.65 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.13 (0.15), residues: 3202 helix: 1.09 (0.16), residues: 1149 sheet: 0.35 (0.24), residues: 483 loop : -0.74 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 8 HIS 0.007 0.001 HIS A 426 PHE 0.038 0.001 PHE B 438 TYR 0.015 0.001 TYR B 336 ARG 0.011 0.000 ARG Q 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 289 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 28 residues processed: 322 average time/residue: 1.5574 time to fit residues: 575.8749 Evaluate side-chains 302 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 274 time to evaluate : 3.243 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 19 residues processed: 9 average time/residue: 0.3961 time to fit residues: 9.9632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 0.1980 chunk 276 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 307 optimal weight: 0.4980 chunk 255 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 272 HIS ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 GLN C 97 ASN C 226 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 26075 Z= 0.308 Angle : 0.741 81.353 35207 Z= 0.327 Chirality : 0.052 1.598 3998 Planarity : 0.004 0.052 4519 Dihedral : 4.100 22.393 3559 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.88 % Allowed : 14.03 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.09 (0.15), residues: 3202 helix: 1.08 (0.16), residues: 1140 sheet: 0.30 (0.23), residues: 491 loop : -0.75 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 8 HIS 0.007 0.001 HIS A 426 PHE 0.013 0.001 PHE B 212 TYR 0.016 0.001 TYR B 336 ARG 0.011 0.000 ARG Q 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 279 time to evaluate : 3.087 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 28 residues processed: 309 average time/residue: 1.4954 time to fit residues: 532.7881 Evaluate side-chains 306 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 278 time to evaluate : 3.099 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 19 residues processed: 9 average time/residue: 0.7341 time to fit residues: 12.8603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 224 optimal weight: 0.0050 chunk 174 optimal weight: 0.8980 chunk 259 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 306 optimal weight: 0.3980 chunk 191 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 272 HIS ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN B1009 GLN C 97 ASN G 6 GLN K 46 ASN P 17 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 26075 Z= 0.170 Angle : 0.709 81.903 35207 Z= 0.308 Chirality : 0.050 1.570 3998 Planarity : 0.004 0.053 4519 Dihedral : 3.874 20.550 3559 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.35 % Allowed : 15.03 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.24 (0.15), residues: 3202 helix: 1.17 (0.16), residues: 1145 sheet: 0.41 (0.23), residues: 501 loop : -0.66 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 8 HIS 0.006 0.001 HIS A 426 PHE 0.010 0.001 PHE C 204 TYR 0.015 0.001 TYR P 28 ARG 0.012 0.000 ARG Q 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 286 time to evaluate : 3.461 Fit side-chains outliers start: 38 outliers final: 18 residues processed: 313 average time/residue: 1.6259 time to fit residues: 587.8787 Evaluate side-chains 285 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 267 time to evaluate : 3.155 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.3007 time to fit residues: 6.0094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 240 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 272 HIS ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN B1009 GLN C 97 ASN G 6 GLN P 17 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 26075 Z= 0.327 Angle : 0.762 82.140 35207 Z= 0.337 Chirality : 0.052 1.585 3998 Planarity : 0.004 0.053 4519 Dihedral : 4.097 22.317 3559 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.43 % Favored : 95.53 % Rotamer: Outliers : 1.67 % Allowed : 15.38 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.10 (0.15), residues: 3202 helix: 1.05 (0.16), residues: 1143 sheet: 0.33 (0.23), residues: 490 loop : -0.73 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1068 HIS 0.007 0.001 HIS A 426 PHE 0.013 0.001 PHE B 212 TYR 0.022 0.001 TYR G 118 ARG 0.013 0.000 ARG Q 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 276 time to evaluate : 3.278 Fit side-chains outliers start: 47 outliers final: 26 residues processed: 303 average time/residue: 1.5651 time to fit residues: 547.8646 Evaluate side-chains 300 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 274 time to evaluate : 3.368 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 19 residues processed: 7 average time/residue: 1.1989 time to fit residues: 14.9518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 267 optimal weight: 4.9990 chunk 285 optimal weight: 0.9990 chunk 171 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 224 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 272 HIS ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 GLN C 97 ASN G 6 GLN K 46 ASN P 17 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 26075 Z= 0.325 Angle : 0.768 82.692 35207 Z= 0.341 Chirality : 0.052 1.557 3998 Planarity : 0.004 0.066 4519 Dihedral : 4.163 22.758 3559 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.28 % Favored : 95.69 % Rotamer: Outliers : 1.35 % Allowed : 15.81 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.02 (0.15), residues: 3202 helix: 0.99 (0.16), residues: 1141 sheet: 0.26 (0.23), residues: 490 loop : -0.77 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1068 HIS 0.007 0.001 HIS A 426 PHE 0.013 0.001 PHE B 212 TYR 0.022 0.001 TYR G 118 ARG 0.018 0.000 ARG P 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 280 time to evaluate : 2.761 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 28 residues processed: 305 average time/residue: 1.5309 time to fit residues: 537.3911 Evaluate side-chains 295 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 267 time to evaluate : 3.014 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 22 residues processed: 6 average time/residue: 0.8585 time to fit residues: 10.6335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.0570 chunk 302 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 209 optimal weight: 0.0670 chunk 316 optimal weight: 4.9990 chunk 291 optimal weight: 0.9990 chunk 252 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 194 optimal weight: 0.5980 chunk 154 optimal weight: 0.9980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 272 HIS ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN B1009 GLN C 97 ASN C 271 GLN G 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.107 26075 Z= 0.162 Angle : 0.722 82.872 35207 Z= 0.316 Chirality : 0.050 1.522 3998 Planarity : 0.004 0.078 4519 Dihedral : 3.866 20.332 3559 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 1.07 % Allowed : 16.41 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.23 (0.15), residues: 3202 helix: 1.16 (0.16), residues: 1142 sheet: 0.40 (0.23), residues: 499 loop : -0.65 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 8 HIS 0.005 0.001 HIS A 426 PHE 0.026 0.001 PHE B 438 TYR 0.021 0.001 TYR G 118 ARG 0.019 0.000 ARG P 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 281 time to evaluate : 2.855 Fit side-chains outliers start: 30 outliers final: 21 residues processed: 307 average time/residue: 1.5091 time to fit residues: 536.9220 Evaluate side-chains 297 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 276 time to evaluate : 3.055 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 20 residues processed: 1 average time/residue: 0.3920 time to fit residues: 4.8636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 3.9990 chunk 268 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 105 optimal weight: 0.1980 chunk 259 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 HIS ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN B1009 GLN C 97 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.118214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.078009 restraints weight = 36448.059| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.47 r_work: 0.2778 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 26075 Z= 0.389 Angle : 0.792 83.527 35207 Z= 0.354 Chirality : 0.053 1.511 3998 Planarity : 0.005 0.088 4519 Dihedral : 4.190 22.762 3559 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.10 % Allowed : 16.70 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3202 helix: 0.95 (0.16), residues: 1144 sheet: 0.26 (0.23), residues: 489 loop : -0.76 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1068 HIS 0.007 0.001 HIS B 993 PHE 0.015 0.002 PHE B 212 TYR 0.023 0.001 TYR G 118 ARG 0.020 0.001 ARG P 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9402.80 seconds wall clock time: 167 minutes 56.12 seconds (10076.12 seconds total)