Starting phenix.real_space_refine on Sun Jun 8 21:50:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fsj_29419/06_2025/8fsj_29419.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fsj_29419/06_2025/8fsj_29419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fsj_29419/06_2025/8fsj_29419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fsj_29419/06_2025/8fsj_29419.map" model { file = "/net/cci-nas-00/data/ceres_data/8fsj_29419/06_2025/8fsj_29419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fsj_29419/06_2025/8fsj_29419.cif" } resolution = 3.65 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= 0.021 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: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 6166 2.51 5 N 1642 2.21 5 O 1996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9855 Number of models: 1 Model: "" Number of chains: 16 Chain: "E" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2235 Classifications: {'peptide': 284} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 260} Chain: "H" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1638 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "L" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1629 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 631 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 6, 'TRANS': 75} Chain breaks: 1 Chain: "B" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1556 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1792 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 224} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.85, per 1000 atoms: 0.70 Number of scatterers: 9855 At special positions: 0 Unit cell: (74.676, 135.128, 137.795, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 1996 8.00 N 1642 7.00 C 6166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS E 429 " - pdb=" SG CYS E 503 " distance=2.05 Simple disulfide: pdb=" SG CYS E 452 " - pdb=" SG CYS E 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 459 " - pdb=" SG CYS E 486 " distance=2.03 Simple disulfide: pdb=" SG CYS E 494 " - pdb=" SG CYS E 564 " distance=2.04 Simple disulfide: pdb=" SG CYS E 508 " - pdb=" SG CYS E 552 " distance=2.03 Simple disulfide: pdb=" SG CYS E 569 " - pdb=" SG CYS E 597 " distance=2.03 Simple disulfide: pdb=" SG CYS E 581 " - pdb=" SG CYS E 585 " distance=2.03 Simple disulfide: pdb=" SG CYS E 607 " - pdb=" SG CYS E 644 " distance=2.04 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 677 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 100 " - pdb=" SG CYS H 100E" distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS A 238 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 401 " - " ASN A 209 " " NAG A 402 " - " ASN A 250 " " NAG D 1 " - " ASN E 430 " " NAG E 801 " - " ASN E 576 " " NAG E 802 " - " ASN E 695 " " NAG E 803 " - " ASN E 532 " " NAG E 804 " - " ASN E 423 " " NAG F 1 " - " ASN E 540 " " NAG G 1 " - " ASN E 448 " " NAG I 1 " - " ASN E 623 " " NAG J 1 " - " ASN E 645 " " NAG K 1 " - " ASN E 556 " " NAG M 1 " - " ASN A 305 " " NAG N 1 " - " ASN A 196 " Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.2 seconds 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 31 sheets defined 8.0% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'E' and resid 438 through 443 removed outlier: 4.023A pdb=" N PHE E 442 " --> pdb=" O LEU E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 450 No H-bonds generated for 'chain 'E' and resid 448 through 450' Processing helix chain 'E' and resid 451 through 456 Processing helix chain 'E' and resid 593 through 598 Processing helix chain 'E' and resid 613 through 618 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.768A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.199A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.678A pdb=" N ASN B 31 " --> pdb=" O VAL B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.157A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 182 through 188 removed outlier: 3.610A pdb=" N HIS B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 186 through 192 removed outlier: 3.595A pdb=" N GLY C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 497 through 498 Processing sheet with id=AA2, first strand: chain 'E' and resid 503 through 509 removed outlier: 4.551A pdb=" N MET E 555 " --> pdb=" O CYS E 503 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N THR E 553 " --> pdb=" O PRO E 505 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N TYR E 507 " --> pdb=" O GLY E 551 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLY E 551 " --> pdb=" O TYR E 507 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 607 through 608 removed outlier: 3.535A pdb=" N THR E 625 " --> pdb=" O CYS E 644 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 629 through 630 Processing sheet with id=AA5, first strand: chain 'E' and resid 658 through 659 removed outlier: 5.809A pdb=" N ASP E 658 " --> pdb=" O PHE E 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 671 through 673 removed outlier: 3.659A pdb=" N GLN E 700 " --> pdb=" O TRP E 672 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N HIS E 691 " --> pdb=" O TYR E 701 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.571A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.563A pdb=" N LYS H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN H 39 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.563A pdb=" N LYS H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N CYS H 92 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG H 94 " --> pdb=" O VAL H 100J" (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.703A pdb=" N LYS H 143 " --> pdb=" O SER H 120 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER H 180 " --> pdb=" O CYS H 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.703A pdb=" N LYS H 143 " --> pdb=" O SER H 120 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LYS H 143 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU H 178 " --> pdb=" O LYS H 143 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL H 169 " --> pdb=" O SER H 177 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 150 through 154 removed outlier: 3.548A pdb=" N SER H 153 " --> pdb=" O ASN H 197 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.593A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 11.946A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 10.664A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 12.034A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.870A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 11.139A pdb=" N GLN L 27 " --> pdb=" O GLU L 70 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N GLU L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY L 68 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.700A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR L 36 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.700A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 116 through 118 removed outlier: 3.692A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 153 through 155 removed outlier: 3.743A pdb=" N GLN L 155 " --> pdb=" O TRP L 148 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 193 through 197 removed outlier: 3.818A pdb=" N HIS A 202 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 197 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 220 through 221 removed outlier: 3.707A pdb=" N ILE A 220 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 229 through 232 removed outlier: 4.309A pdb=" N VAL A 230 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG A 237 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 5 through 7 removed outlier: 4.176A pdb=" N SER B 22 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS B 23 " --> pdb=" O PHE B 71 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE B 71 " --> pdb=" O CYS B 23 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.608A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 114 through 118 removed outlier: 3.524A pdb=" N SER B 114 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN B 137 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 133 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TYR B 172 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 144 through 149 removed outlier: 3.766A pdb=" N VAL B 204 " --> pdb=" O VAL B 195 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 6 through 6A Processing sheet with id=AC8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.707A pdb=" N GLU C 10 " --> pdb=" O ILE C 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 46 through 50 removed outlier: 6.871A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 70 through 72 removed outlier: 3.523A pdb=" N SER C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.826A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.826A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C 175 " --> pdb=" O GLN C 171 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 151 through 153 removed outlier: 3.742A pdb=" N THR C 151 " --> pdb=" O ASN C 199 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR C 194 " --> pdb=" O VAL C 211 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 657 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: 3.29 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3121 1.35 - 1.47: 2624 1.47 - 1.59: 4291 1.59 - 1.71: 0 1.71 - 1.83: 60 Bond restraints: 10096 Sorted by residual: bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N LEU B 2 " pdb=" CA LEU B 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N GLN C 3 " pdb=" CA GLN C 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N HIS E 421 " pdb=" CA HIS E 421 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 ... (remaining 10091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 13212 1.54 - 3.07: 447 3.07 - 4.61: 92 4.61 - 6.14: 22 6.14 - 7.68: 6 Bond angle restraints: 13779 Sorted by residual: angle pdb=" C SER C 156 " pdb=" CA SER C 156 " pdb=" CB SER C 156 " ideal model delta sigma weight residual 116.54 110.82 5.72 1.15e+00 7.56e-01 2.47e+01 angle pdb=" N GLY C 100O" pdb=" CA GLY C 100O" pdb=" C GLY C 100O" ideal model delta sigma weight residual 113.18 120.86 -7.68 2.37e+00 1.78e-01 1.05e+01 angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" CB ALA L 51 " ideal model delta sigma weight residual 114.17 110.48 3.69 1.14e+00 7.69e-01 1.05e+01 angle pdb=" CA LEU E 689 " pdb=" C LEU E 689 " pdb=" O LEU E 689 " ideal model delta sigma weight residual 121.50 117.91 3.59 1.25e+00 6.40e-01 8.25e+00 angle pdb=" CA SER C 156 " pdb=" C SER C 156 " pdb=" N GLY C 157 " ideal model delta sigma weight residual 119.52 117.31 2.21 7.90e-01 1.60e+00 7.81e+00 ... (remaining 13774 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 5867 21.62 - 43.24: 379 43.24 - 64.85: 60 64.85 - 86.47: 48 86.47 - 108.09: 26 Dihedral angle restraints: 6380 sinusoidal: 2769 harmonic: 3611 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual -86.00 -172.67 86.67 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual -86.00 -169.95 83.95 1 1.00e+01 1.00e-02 8.59e+01 dihedral pdb=" CB CYS E 429 " pdb=" SG CYS E 429 " pdb=" SG CYS E 503 " pdb=" CB CYS E 503 " ideal model delta sinusoidal sigma weight residual 93.00 23.51 69.49 1 1.00e+01 1.00e-02 6.24e+01 ... (remaining 6377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1357 0.055 - 0.110: 213 0.110 - 0.165: 55 0.165 - 0.220: 2 0.220 - 0.275: 7 Chirality restraints: 1634 Sorted by residual: chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1631 not shown) Planarity restraints: 1746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 52I" 0.053 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO C 52J" -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 52J" 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 52J" 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 646 " 0.013 2.00e-02 2.50e+03 1.57e-02 6.20e+00 pdb=" CG TRP E 646 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP E 646 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP E 646 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 646 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 646 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 646 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 646 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 646 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP E 646 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 148 " -0.039 5.00e-02 4.00e+02 5.82e-02 5.41e+00 pdb=" N PRO H 149 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO H 149 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 149 " -0.029 5.00e-02 4.00e+02 ... (remaining 1743 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 107 2.56 - 3.14: 8370 3.14 - 3.73: 14219 3.73 - 4.31: 19492 4.31 - 4.90: 32530 Nonbonded interactions: 74718 Sorted by model distance: nonbonded pdb=" O ALA A 251 " pdb=" OG1 THR A 255 " model vdw 1.974 3.040 nonbonded pdb=" OD1 ASP A 233 " pdb=" OG SER A 235 " model vdw 2.021 3.040 nonbonded pdb=" O TYR B 185 " pdb=" OH TYR B 191 " model vdw 2.037 3.040 nonbonded pdb=" NE2 GLN C 192 " pdb=" O THR C 193 " model vdw 2.047 3.120 nonbonded pdb=" NH2 ARG L 61 " pdb=" O SER L 77 " model vdw 2.064 3.120 ... (remaining 74713 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 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' } 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=0.00 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: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.310 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 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 0.034 10145 Z= 0.194 Angle : 0.701 7.679 13905 Z= 0.349 Chirality : 0.049 0.275 1634 Planarity : 0.005 0.079 1732 Dihedral : 16.992 108.091 4009 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.24), residues: 1241 helix: -0.85 (0.82), residues: 48 sheet: -0.05 (0.26), residues: 426 loop : -1.20 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 646 HIS 0.006 0.001 HIS C 95 PHE 0.007 0.001 PHE H 146 TYR 0.021 0.001 TYR C 52I ARG 0.020 0.001 ARG E 543 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 14) link_NAG-ASN : angle 1.85349 ( 42) link_BETA1-4 : bond 0.00341 ( 14) link_BETA1-4 : angle 1.22524 ( 42) hydrogen bonds : bond 0.27125 ( 244) hydrogen bonds : angle 11.09980 ( 657) SS BOND : bond 0.00471 ( 21) SS BOND : angle 1.51281 ( 42) covalent geometry : bond 0.00409 (10096) covalent geometry : angle 0.68837 (13779) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 431 ASP cc_start: 0.7749 (t0) cc_final: 0.7415 (t0) REVERT: E 546 GLN cc_start: 0.7942 (pp30) cc_final: 0.7291 (pp30) REVERT: H 91 TYR cc_start: 0.7205 (m-80) cc_final: 0.6275 (m-10) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2354 time to fit residues: 50.4492 Evaluate side-chains 116 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 467 GLN H 31 ASN H 55 ASN B 89 GLN B 146 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.208078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.164542 restraints weight = 13733.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.161330 restraints weight = 20621.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.163438 restraints weight = 19871.131| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10145 Z= 0.171 Angle : 0.719 9.004 13905 Z= 0.359 Chirality : 0.047 0.194 1634 Planarity : 0.005 0.063 1732 Dihedral : 11.851 69.775 1927 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.14 % Allowed : 7.34 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.05 (0.24), residues: 1241 helix: -1.37 (0.72), residues: 50 sheet: -0.00 (0.26), residues: 418 loop : -1.07 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 646 HIS 0.005 0.001 HIS E 589 PHE 0.019 0.002 PHE L 139 TYR 0.020 0.002 TYR C 194 ARG 0.005 0.001 ARG E 543 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 14) link_NAG-ASN : angle 1.97566 ( 42) link_BETA1-4 : bond 0.00508 ( 14) link_BETA1-4 : angle 1.99051 ( 42) hydrogen bonds : bond 0.04835 ( 244) hydrogen bonds : angle 7.96504 ( 657) SS BOND : bond 0.00385 ( 21) SS BOND : angle 1.20701 ( 42) covalent geometry : bond 0.00405 (10096) covalent geometry : angle 0.70213 (13779) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7999 (pp30) cc_final: 0.7383 (pp30) REVERT: E 656 ASP cc_start: 0.7701 (t0) cc_final: 0.7375 (t0) REVERT: H 91 TYR cc_start: 0.7155 (m-80) cc_final: 0.6921 (m-80) REVERT: A 309 TYR cc_start: 0.5467 (p90) cc_final: 0.4945 (p90) outliers start: 12 outliers final: 7 residues processed: 140 average time/residue: 0.2190 time to fit residues: 43.3932 Evaluate side-chains 125 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 0.0270 chunk 94 optimal weight: 7.9990 overall best weight: 1.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 467 GLN ** E 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 ASN ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.204692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.143217 restraints weight = 13988.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.142700 restraints weight = 11633.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.142866 restraints weight = 10478.531| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 10145 Z= 0.256 Angle : 0.787 10.946 13905 Z= 0.393 Chirality : 0.051 0.211 1634 Planarity : 0.006 0.059 1732 Dihedral : 7.981 46.701 1927 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.48 % Allowed : 12.30 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.52 (0.23), residues: 1241 helix: -1.61 (0.69), residues: 50 sheet: -0.36 (0.24), residues: 442 loop : -1.40 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 646 HIS 0.005 0.001 HIS E 589 PHE 0.027 0.002 PHE E 509 TYR 0.024 0.002 TYR B 91 ARG 0.005 0.001 ARG B 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 14) link_NAG-ASN : angle 2.27026 ( 42) link_BETA1-4 : bond 0.00468 ( 14) link_BETA1-4 : angle 2.11344 ( 42) hydrogen bonds : bond 0.04221 ( 244) hydrogen bonds : angle 7.22687 ( 657) SS BOND : bond 0.00453 ( 21) SS BOND : angle 1.48712 ( 42) covalent geometry : bond 0.00613 (10096) covalent geometry : angle 0.76791 (13779) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7964 (pp30) cc_final: 0.7371 (pp30) REVERT: E 610 ASP cc_start: 0.8229 (t0) cc_final: 0.7591 (t70) REVERT: E 656 ASP cc_start: 0.8163 (t0) cc_final: 0.7881 (t0) REVERT: L 27 GLN cc_start: 0.6444 (tm-30) cc_final: 0.6193 (tm-30) REVERT: L 139 PHE cc_start: 0.7171 (p90) cc_final: 0.6738 (p90) REVERT: B 123 GLU cc_start: 0.8679 (tp30) cc_final: 0.8411 (mp0) REVERT: B 139 PHE cc_start: 0.7274 (p90) cc_final: 0.6806 (p90) outliers start: 26 outliers final: 16 residues processed: 144 average time/residue: 0.2476 time to fit residues: 49.7485 Evaluate side-chains 136 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 699 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 20 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 33 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 62 optimal weight: 9.9990 chunk 22 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 638 HIS H 55 ASN ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.207002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.160072 restraints weight = 13660.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.155214 restraints weight = 17265.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.157039 restraints weight = 19111.000| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10145 Z= 0.128 Angle : 0.664 9.603 13905 Z= 0.328 Chirality : 0.045 0.206 1634 Planarity : 0.005 0.058 1732 Dihedral : 6.260 52.016 1927 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.00 % Allowed : 14.01 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.30 (0.23), residues: 1241 helix: -1.56 (0.71), residues: 50 sheet: -0.16 (0.25), residues: 423 loop : -1.26 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP E 646 HIS 0.002 0.001 HIS E 589 PHE 0.013 0.001 PHE E 509 TYR 0.015 0.001 TYR C 194 ARG 0.006 0.001 ARG E 630 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 14) link_NAG-ASN : angle 1.88515 ( 42) link_BETA1-4 : bond 0.00421 ( 14) link_BETA1-4 : angle 1.77273 ( 42) hydrogen bonds : bond 0.03303 ( 244) hydrogen bonds : angle 6.72805 ( 657) SS BOND : bond 0.00287 ( 21) SS BOND : angle 0.97583 ( 42) covalent geometry : bond 0.00303 (10096) covalent geometry : angle 0.64942 (13779) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7949 (pp30) cc_final: 0.7372 (pp30) REVERT: E 610 ASP cc_start: 0.8040 (t0) cc_final: 0.7590 (t70) REVERT: A 219 MET cc_start: 0.7131 (tpp) cc_final: 0.6348 (ppp) REVERT: B 4 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7940 (mm) REVERT: B 123 GLU cc_start: 0.8608 (tp30) cc_final: 0.8314 (mp0) REVERT: B 185 TYR cc_start: 0.6183 (t80) cc_final: 0.5427 (t80) REVERT: B 191 TYR cc_start: 0.4040 (m-80) cc_final: 0.3168 (m-80) REVERT: C 194 TYR cc_start: 0.3515 (OUTLIER) cc_final: 0.1990 (m-80) outliers start: 21 outliers final: 14 residues processed: 151 average time/residue: 0.2454 time to fit residues: 53.0264 Evaluate side-chains 144 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 555 MET Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 607 CYS Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 194 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 118 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 98 optimal weight: 30.0000 chunk 95 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.201518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.157813 restraints weight = 13831.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.159347 restraints weight = 25924.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.160396 restraints weight = 16374.171| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 10145 Z= 0.321 Angle : 0.822 11.356 13905 Z= 0.412 Chirality : 0.051 0.225 1634 Planarity : 0.006 0.062 1732 Dihedral : 6.546 39.386 1927 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 3.91 % Allowed : 14.87 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.78 (0.23), residues: 1241 helix: -1.65 (0.70), residues: 50 sheet: -0.52 (0.25), residues: 431 loop : -1.59 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP E 646 HIS 0.008 0.002 HIS C 95 PHE 0.024 0.003 PHE E 437 TYR 0.027 0.002 TYR B 91 ARG 0.005 0.001 ARG E 543 Details of bonding type rmsd link_NAG-ASN : bond 0.00663 ( 14) link_NAG-ASN : angle 2.25292 ( 42) link_BETA1-4 : bond 0.00433 ( 14) link_BETA1-4 : angle 1.84372 ( 42) hydrogen bonds : bond 0.03934 ( 244) hydrogen bonds : angle 6.89882 ( 657) SS BOND : bond 0.00561 ( 21) SS BOND : angle 1.47803 ( 42) covalent geometry : bond 0.00766 (10096) covalent geometry : angle 0.80563 (13779) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.8003 (pp30) cc_final: 0.7441 (pp30) REVERT: L 27 GLN cc_start: 0.6511 (tm-30) cc_final: 0.5944 (tm-30) REVERT: L 47 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8318 (mt) REVERT: L 50 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7175 (mptt) REVERT: L 82 ASP cc_start: 0.6772 (t0) cc_final: 0.6305 (t0) REVERT: A 219 MET cc_start: 0.7124 (tpp) cc_final: 0.6401 (ppp) REVERT: B 4 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8064 (mm) REVERT: B 185 TYR cc_start: 0.5909 (t80) cc_final: 0.5051 (t80) REVERT: B 191 TYR cc_start: 0.3701 (m-80) cc_final: 0.3177 (m-80) REVERT: C 100 MET cc_start: 0.7904 (ttm) cc_final: 0.7586 (ttm) outliers start: 41 outliers final: 29 residues processed: 160 average time/residue: 0.2484 time to fit residues: 58.2891 Evaluate side-chains 153 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 548 ASN Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 607 CYS Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 629 VAL Chi-restraints excluded: chain E residue 699 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 169 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 32 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 37 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 114 optimal weight: 0.0170 chunk 118 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.207671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.161635 restraints weight = 13796.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.159140 restraints weight = 20321.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.162060 restraints weight = 17235.206| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10145 Z= 0.127 Angle : 0.657 9.879 13905 Z= 0.329 Chirality : 0.045 0.203 1634 Planarity : 0.005 0.063 1732 Dihedral : 5.709 44.826 1927 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.38 % Allowed : 17.45 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.23), residues: 1241 helix: -1.74 (0.68), residues: 51 sheet: -0.33 (0.25), residues: 431 loop : -1.35 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP E 646 HIS 0.003 0.001 HIS E 589 PHE 0.019 0.002 PHE L 139 TYR 0.013 0.001 TYR C 194 ARG 0.006 0.001 ARG B 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 14) link_NAG-ASN : angle 1.79141 ( 42) link_BETA1-4 : bond 0.00458 ( 14) link_BETA1-4 : angle 1.47848 ( 42) hydrogen bonds : bond 0.02993 ( 244) hydrogen bonds : angle 6.40225 ( 657) SS BOND : bond 0.00327 ( 21) SS BOND : angle 1.03586 ( 42) covalent geometry : bond 0.00298 (10096) covalent geometry : angle 0.64523 (13779) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7945 (pp30) cc_final: 0.7377 (pp30) REVERT: L 27 GLN cc_start: 0.6545 (tm-30) cc_final: 0.6111 (tm-30) REVERT: L 82 ASP cc_start: 0.6669 (t0) cc_final: 0.6286 (t0) REVERT: B 4 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7972 (mm) REVERT: B 96 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8046 (pt) REVERT: B 191 TYR cc_start: 0.3968 (m-80) cc_final: 0.3413 (m-80) REVERT: C 100 MET cc_start: 0.7905 (ttm) cc_final: 0.7543 (ttm) outliers start: 25 outliers final: 17 residues processed: 158 average time/residue: 0.2099 time to fit residues: 47.4075 Evaluate side-chains 146 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 555 MET Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 607 CYS Chi-restraints excluded: chain E residue 677 CYS Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 20 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 24 optimal weight: 0.0870 chunk 64 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 123 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.207050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.164892 restraints weight = 13901.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.167334 restraints weight = 23705.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.168104 restraints weight = 15339.506| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10145 Z= 0.143 Angle : 0.659 9.578 13905 Z= 0.330 Chirality : 0.045 0.192 1634 Planarity : 0.005 0.061 1732 Dihedral : 5.582 47.298 1927 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.05 % Allowed : 17.45 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.36 (0.23), residues: 1241 helix: -1.54 (0.70), residues: 50 sheet: -0.27 (0.25), residues: 431 loop : -1.25 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E 646 HIS 0.003 0.001 HIS C 95 PHE 0.015 0.001 PHE L 118 TYR 0.011 0.001 TYR C 194 ARG 0.005 0.000 ARG E 630 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 14) link_NAG-ASN : angle 1.78123 ( 42) link_BETA1-4 : bond 0.00411 ( 14) link_BETA1-4 : angle 1.45431 ( 42) hydrogen bonds : bond 0.02927 ( 244) hydrogen bonds : angle 6.33031 ( 657) SS BOND : bond 0.00342 ( 21) SS BOND : angle 1.04811 ( 42) covalent geometry : bond 0.00345 (10096) covalent geometry : angle 0.64700 (13779) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7956 (pp30) cc_final: 0.7352 (pp30) REVERT: E 644 CYS cc_start: 0.6637 (t) cc_final: 0.6250 (t) REVERT: L 82 ASP cc_start: 0.6666 (t0) cc_final: 0.6216 (t0) REVERT: B 4 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7938 (mm) REVERT: B 96 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.8004 (pt) REVERT: B 191 TYR cc_start: 0.3742 (m-80) cc_final: 0.3401 (m-80) REVERT: C 100 MET cc_start: 0.7858 (ttm) cc_final: 0.7477 (ttm) outliers start: 32 outliers final: 23 residues processed: 153 average time/residue: 0.1935 time to fit residues: 42.9929 Evaluate side-chains 149 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 607 CYS Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 629 VAL Chi-restraints excluded: chain E residue 677 CYS Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 169 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 119 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.208620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.167326 restraints weight = 14093.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.171445 restraints weight = 23848.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.171410 restraints weight = 12088.308| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10145 Z= 0.132 Angle : 0.641 9.225 13905 Z= 0.318 Chirality : 0.044 0.184 1634 Planarity : 0.005 0.061 1732 Dihedral : 5.422 52.267 1927 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.15 % Allowed : 17.25 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.29 (0.23), residues: 1241 helix: -1.37 (0.70), residues: 50 sheet: -0.23 (0.25), residues: 431 loop : -1.21 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 646 HIS 0.003 0.001 HIS E 589 PHE 0.019 0.002 PHE L 139 TYR 0.011 0.001 TYR C 194 ARG 0.007 0.000 ARG B 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 14) link_NAG-ASN : angle 1.69426 ( 42) link_BETA1-4 : bond 0.00420 ( 14) link_BETA1-4 : angle 1.39872 ( 42) hydrogen bonds : bond 0.02796 ( 244) hydrogen bonds : angle 6.13662 ( 657) SS BOND : bond 0.00340 ( 21) SS BOND : angle 1.00638 ( 42) covalent geometry : bond 0.00317 (10096) covalent geometry : angle 0.62979 (13779) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7856 (pp30) cc_final: 0.7254 (pp30) REVERT: E 644 CYS cc_start: 0.6743 (t) cc_final: 0.6400 (t) REVERT: L 27 GLN cc_start: 0.6498 (tm-30) cc_final: 0.6102 (tm-30) REVERT: B 4 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7880 (mm) REVERT: B 96 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8053 (pt) REVERT: B 191 TYR cc_start: 0.3804 (m-80) cc_final: 0.3531 (m-80) REVERT: C 100 MET cc_start: 0.7899 (ttm) cc_final: 0.7525 (ttm) REVERT: C 204 ASN cc_start: 0.6293 (t0) cc_final: 0.6032 (t0) outliers start: 33 outliers final: 25 residues processed: 157 average time/residue: 0.1879 time to fit residues: 43.4478 Evaluate side-chains 151 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 555 MET Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 607 CYS Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 629 VAL Chi-restraints excluded: chain E residue 677 CYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 169 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 638 HIS H 55 ASN ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.206341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.162477 restraints weight = 13669.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.162165 restraints weight = 23353.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.164480 restraints weight = 17279.709| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10145 Z= 0.160 Angle : 0.662 9.400 13905 Z= 0.331 Chirality : 0.045 0.174 1634 Planarity : 0.005 0.060 1732 Dihedral : 5.504 53.078 1927 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.24 % Allowed : 17.25 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.29 (0.23), residues: 1241 helix: -1.53 (0.67), residues: 50 sheet: -0.21 (0.25), residues: 429 loop : -1.21 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 646 HIS 0.004 0.001 HIS C 95 PHE 0.016 0.002 PHE E 509 TYR 0.014 0.001 TYR B 91 ARG 0.005 0.000 ARG E 630 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 14) link_NAG-ASN : angle 1.73753 ( 42) link_BETA1-4 : bond 0.00414 ( 14) link_BETA1-4 : angle 1.41959 ( 42) hydrogen bonds : bond 0.02905 ( 244) hydrogen bonds : angle 6.10476 ( 657) SS BOND : bond 0.00357 ( 21) SS BOND : angle 1.08608 ( 42) covalent geometry : bond 0.00388 (10096) covalent geometry : angle 0.65065 (13779) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7791 (pp30) cc_final: 0.7187 (pp30) REVERT: E 644 CYS cc_start: 0.6761 (t) cc_final: 0.6359 (t) REVERT: L 38 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8146 (tm-30) REVERT: B 4 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7905 (mm) REVERT: B 96 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.8036 (pt) REVERT: B 191 TYR cc_start: 0.4086 (m-80) cc_final: 0.3699 (m-80) REVERT: C 59 TYR cc_start: 0.8489 (m-80) cc_final: 0.8260 (m-80) REVERT: C 100 MET cc_start: 0.7933 (ttm) cc_final: 0.7554 (ttm) outliers start: 34 outliers final: 29 residues processed: 150 average time/residue: 0.1989 time to fit residues: 44.6333 Evaluate side-chains 151 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 555 MET Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 607 CYS Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 629 VAL Chi-restraints excluded: chain E residue 677 CYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 66 optimal weight: 4.9990 chunk 26 optimal weight: 0.0010 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.207349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.164120 restraints weight = 13848.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.164041 restraints weight = 22546.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.165490 restraints weight = 18345.278| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10145 Z= 0.144 Angle : 0.651 9.345 13905 Z= 0.326 Chirality : 0.045 0.178 1634 Planarity : 0.005 0.061 1732 Dihedral : 5.448 56.162 1927 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.96 % Allowed : 17.45 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.25 (0.24), residues: 1241 helix: -1.34 (0.71), residues: 50 sheet: -0.18 (0.25), residues: 429 loop : -1.20 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP E 646 HIS 0.003 0.001 HIS C 95 PHE 0.018 0.002 PHE L 139 TYR 0.012 0.001 TYR B 91 ARG 0.005 0.000 ARG E 630 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 14) link_NAG-ASN : angle 1.69614 ( 42) link_BETA1-4 : bond 0.00414 ( 14) link_BETA1-4 : angle 1.37939 ( 42) hydrogen bonds : bond 0.02791 ( 244) hydrogen bonds : angle 6.00898 ( 657) SS BOND : bond 0.00347 ( 21) SS BOND : angle 1.03289 ( 42) covalent geometry : bond 0.00347 (10096) covalent geometry : angle 0.64021 (13779) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7777 (pp30) cc_final: 0.7153 (pp30) REVERT: E 644 CYS cc_start: 0.6749 (t) cc_final: 0.6338 (t) REVERT: L 38 GLN cc_start: 0.8327 (tm-30) cc_final: 0.8093 (tm-30) REVERT: A 219 MET cc_start: 0.5741 (tpt) cc_final: 0.5513 (ppp) REVERT: B 4 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7896 (mm) REVERT: B 96 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8051 (pt) REVERT: B 191 TYR cc_start: 0.4134 (m-80) cc_final: 0.3810 (m-80) REVERT: C 59 TYR cc_start: 0.8502 (m-80) cc_final: 0.8268 (m-80) REVERT: C 100 MET cc_start: 0.7953 (ttm) cc_final: 0.7572 (ttm) outliers start: 31 outliers final: 27 residues processed: 150 average time/residue: 0.1895 time to fit residues: 42.0251 Evaluate side-chains 150 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 555 MET Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 607 CYS Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 629 VAL Chi-restraints excluded: chain E residue 677 CYS Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 0.0170 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 90 optimal weight: 10.0000 chunk 123 optimal weight: 0.0980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.208692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.163903 restraints weight = 13949.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.161186 restraints weight = 19501.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.162527 restraints weight = 20366.515| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10145 Z= 0.137 Angle : 0.909 59.198 13905 Z= 0.502 Chirality : 0.045 0.181 1634 Planarity : 0.005 0.064 1732 Dihedral : 5.467 56.150 1927 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.76 % Allowed : 17.73 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.26 (0.24), residues: 1241 helix: -1.33 (0.71), residues: 50 sheet: -0.20 (0.25), residues: 431 loop : -1.20 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP E 646 HIS 0.003 0.001 HIS C 95 PHE 0.012 0.001 PHE L 118 TYR 0.010 0.001 TYR B 91 ARG 0.013 0.001 ARG B 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 14) link_NAG-ASN : angle 1.68814 ( 42) link_BETA1-4 : bond 0.00399 ( 14) link_BETA1-4 : angle 1.37319 ( 42) hydrogen bonds : bond 0.02769 ( 244) hydrogen bonds : angle 6.00651 ( 657) SS BOND : bond 0.00316 ( 21) SS BOND : angle 1.01447 ( 42) covalent geometry : bond 0.00308 (10096) covalent geometry : angle 0.90349 (13779) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3573.77 seconds wall clock time: 65 minutes 21.56 seconds (3921.56 seconds total)