Starting phenix.real_space_refine on Sun Jul 21 02:35:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7h_41092/07_2024/8t7h_41092.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7h_41092/07_2024/8t7h_41092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7h_41092/07_2024/8t7h_41092.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7h_41092/07_2024/8t7h_41092.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7h_41092/07_2024/8t7h_41092.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7h_41092/07_2024/8t7h_41092.cif" } resolution = 3.3 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= 0.005 sd= 0.032 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 104 5.16 5 C 8288 2.51 5 N 2247 2.21 5 O 2461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 560": "OD1" <-> "OD2" Residue "A PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 560": "OD1" <-> "OD2" Residue "B PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13100 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5614 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 741} Chain breaks: 2 Unresolved non-hydrogen bonds: 508 Unresolved non-hydrogen angles: 638 Unresolved non-hydrogen dihedrals: 421 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 10, 'GLU:plan': 15, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 268 Chain: "B" Number of atoms: 5618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5618 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 741} Chain breaks: 2 Unresolved non-hydrogen bonds: 504 Unresolved non-hydrogen angles: 634 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 10, 'GLU:plan': 15, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 268 Chain: "C" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 920 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 922 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.40, per 1000 atoms: 0.64 Number of scatterers: 13100 At special positions: 0 Unit cell: (87.769, 121.099, 211.09, 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 104 16.00 O 2461 8.00 N 2247 7.00 C 8288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.02 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.02 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 98 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.99 Conformation dependent library (CDL) restraints added in 2.4 seconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3328 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 43.6% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 65 through 82 Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.658A pdb=" N ALA A 105 " --> pdb=" O HIS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 removed outlier: 3.518A pdb=" N GLU A 122 " --> pdb=" O ILE A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.728A pdb=" N GLN A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 209 removed outlier: 3.523A pdb=" N TYR A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 237 removed outlier: 3.859A pdb=" N LYS A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 removed outlier: 4.061A pdb=" N ASP A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 294 Processing helix chain 'A' and resid 304 through 308 removed outlier: 3.560A pdb=" N TRP A 307 " --> pdb=" O SER A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 removed outlier: 3.880A pdb=" N ASP A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 342 " --> pdb=" O ASP A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 344 No H-bonds generated for 'chain 'A' and resid 343 through 344' Processing helix chain 'A' and resid 345 through 349 removed outlier: 3.727A pdb=" N ASN A 349 " --> pdb=" O PRO A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 396 through 419 removed outlier: 3.693A pdb=" N VAL A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 433 through 442 Processing helix chain 'A' and resid 577 through 604 removed outlier: 3.932A pdb=" N TYR A 604 " --> pdb=" O VAL A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 614 through 633 removed outlier: 3.658A pdb=" N PHE A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 673 removed outlier: 3.592A pdb=" N GLY A 652 " --> pdb=" O ARG A 648 " (cutoff:3.500A) Proline residue: A 655 - end of helix removed outlier: 3.673A pdb=" N SER A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ALA A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 662 " --> pdb=" O SER A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 715 Processing helix chain 'A' and resid 736 through 761 Proline residue: A 743 - end of helix Processing helix chain 'A' and resid 765 through 789 removed outlier: 5.714A pdb=" N ALA A 771 " --> pdb=" O ASN A 767 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LYS A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 794 Processing helix chain 'A' and resid 797 through 827 removed outlier: 4.313A pdb=" N VAL A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) Proline residue: A 820 - end of helix Processing helix chain 'B' and resid 65 through 82 Processing helix chain 'B' and resid 101 through 118 removed outlier: 3.960A pdb=" N ILE B 118 " --> pdb=" O ARG B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.629A pdb=" N GLN B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.762A pdb=" N SER B 180 " --> pdb=" O MET B 177 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP B 181 " --> pdb=" O ASP B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 181' Processing helix chain 'B' and resid 197 through 209 removed outlier: 3.509A pdb=" N TYR B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 237 removed outlier: 3.915A pdb=" N LYS B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 266 removed outlier: 4.194A pdb=" N ASP B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 260 " --> pdb=" O SER B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 294 Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.529A pdb=" N TRP B 307 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 342 removed outlier: 3.875A pdb=" N ASP B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 344 No H-bonds generated for 'chain 'B' and resid 343 through 344' Processing helix chain 'B' and resid 345 through 349 removed outlier: 3.725A pdb=" N ASN B 349 " --> pdb=" O PRO B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 Processing helix chain 'B' and resid 396 through 419 removed outlier: 3.697A pdb=" N VAL B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 577 through 604 removed outlier: 4.060A pdb=" N TYR B 604 " --> pdb=" O VAL B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 614 through 633 removed outlier: 3.637A pdb=" N PHE B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 673 Proline residue: B 655 - end of helix removed outlier: 3.573A pdb=" N SER B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU B 662 " --> pdb=" O SER B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 715 Processing helix chain 'B' and resid 736 through 761 Proline residue: B 743 - end of helix Processing helix chain 'B' and resid 765 through 789 removed outlier: 5.706A pdb=" N ALA B 771 " --> pdb=" O ASN B 767 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYS B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR B 773 " --> pdb=" O ASN B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 827 removed outlier: 3.504A pdb=" N ALA B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL B 819 " --> pdb=" O GLY B 815 " (cutoff:3.500A) Proline residue: B 820 - end of helix Processing helix chain 'C' and resid 30 through 34 removed outlier: 3.544A pdb=" N SER C 33 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR C 34 " --> pdb=" O PHE C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 34' Processing helix chain 'C' and resid 64 through 67 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.516A pdb=" N SER D 33 " --> pdb=" O THR D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 67 Processing helix chain 'D' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 217 removed outlier: 3.712A pdb=" N ALA A 275 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 325 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 327 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 446 through 447 Processing sheet with id=AA5, first strand: chain 'A' and resid 521 through 523 Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 558 Processing sheet with id=AA8, first strand: chain 'A' and resid 570 through 571 removed outlier: 4.145A pdb=" N LEU A 731 " --> pdb=" O GLN A 571 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.389A pdb=" N ILE B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLU B 94 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AB2, first strand: chain 'B' and resid 241 through 242 removed outlier: 6.587A pdb=" N CYS B 241 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ALA B 216 " --> pdb=" O CYS B 241 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL B 273 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 275 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 325 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 327 " --> pdb=" O GLY B 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 446 through 447 Processing sheet with id=AB4, first strand: chain 'B' and resid 521 through 523 Processing sheet with id=AB5, first strand: chain 'B' and resid 541 through 543 Processing sheet with id=AB6, first strand: chain 'B' and resid 556 through 558 Processing sheet with id=AB7, first strand: chain 'B' and resid 570 through 571 removed outlier: 4.019A pdb=" N LEU B 731 " --> pdb=" O GLN B 571 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 6 through 9 Processing sheet with id=AB9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.912A pdb=" N MET C 36 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA C 52 " --> pdb=" O MET C 36 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP C 38 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 6 through 9 Processing sheet with id=AC2, first strand: chain 'D' and resid 13 through 14 removed outlier: 6.918A pdb=" N MET D 36 " --> pdb=" O ALA D 52 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ALA D 52 " --> pdb=" O MET D 36 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP D 38 " --> pdb=" O VAL D 50 " (cutoff:3.500A) 654 hydrogen bonds defined for protein. 1842 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: 4.69 Time building geometry restraints manager: 5.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2170 1.31 - 1.43: 3633 1.43 - 1.56: 7433 1.56 - 1.69: 0 1.69 - 1.82: 152 Bond restraints: 13388 Sorted by residual: bond pdb=" C05 QUS A 901 " pdb=" N15 QUS A 901 " ideal model delta sigma weight residual 1.365 1.438 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C05 QUS B 901 " pdb=" N15 QUS B 901 " ideal model delta sigma weight residual 1.365 1.437 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C05 QUS A 901 " pdb=" O20 QUS A 901 " ideal model delta sigma weight residual 1.362 1.420 -0.058 2.00e-02 2.50e+03 8.49e+00 bond pdb=" C05 QUS B 901 " pdb=" O20 QUS B 901 " ideal model delta sigma weight residual 1.362 1.420 -0.058 2.00e-02 2.50e+03 8.41e+00 bond pdb=" C04 QUS A 901 " pdb=" N14 QUS A 901 " ideal model delta sigma weight residual 1.380 1.438 -0.058 2.00e-02 2.50e+03 8.35e+00 ... (remaining 13383 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.80: 381 106.80 - 113.61: 7289 113.61 - 120.43: 4962 120.43 - 127.24: 5455 127.24 - 134.06: 156 Bond angle restraints: 18243 Sorted by residual: angle pdb=" C03 QUS A 901 " pdb=" N14 QUS A 901 " pdb=" O20 QUS A 901 " ideal model delta sigma weight residual 112.77 126.07 -13.30 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C03 QUS B 901 " pdb=" N14 QUS B 901 " pdb=" O20 QUS B 901 " ideal model delta sigma weight residual 112.77 126.06 -13.29 3.00e+00 1.11e-01 1.96e+01 angle pdb=" C LEU B 711 " pdb=" N PHE B 712 " pdb=" CA PHE B 712 " ideal model delta sigma weight residual 122.06 116.38 5.68 1.86e+00 2.89e-01 9.32e+00 angle pdb=" CB MET A 802 " pdb=" CG MET A 802 " pdb=" SD MET A 802 " ideal model delta sigma weight residual 112.70 121.08 -8.38 3.00e+00 1.11e-01 7.81e+00 angle pdb=" N GLN A 360 " pdb=" CA GLN A 360 " pdb=" CB GLN A 360 " ideal model delta sigma weight residual 110.28 114.58 -4.30 1.55e+00 4.16e-01 7.68e+00 ... (remaining 18238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7195 17.93 - 35.86: 628 35.86 - 53.80: 109 53.80 - 71.73: 11 71.73 - 89.66: 8 Dihedral angle restraints: 7951 sinusoidal: 2761 harmonic: 5190 Sorted by residual: dihedral pdb=" CB CYS B 515 " pdb=" SG CYS B 515 " pdb=" SG CYS B 534 " pdb=" CB CYS B 534 " ideal model delta sinusoidal sigma weight residual 93.00 -177.69 -89.31 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS A 515 " pdb=" SG CYS A 515 " pdb=" SG CYS A 534 " pdb=" CB CYS A 534 " ideal model delta sinusoidal sigma weight residual 93.00 175.16 -82.16 1 1.00e+01 1.00e-02 8.29e+01 dihedral pdb=" CB CYS A 511 " pdb=" SG CYS A 511 " pdb=" SG CYS A 531 " pdb=" CB CYS A 531 " ideal model delta sinusoidal sigma weight residual 93.00 25.10 67.90 1 1.00e+01 1.00e-02 5.99e+01 ... (remaining 7948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1204 0.033 - 0.065: 595 0.065 - 0.098: 188 0.098 - 0.131: 74 0.131 - 0.163: 6 Chirality restraints: 2067 Sorted by residual: chirality pdb=" CA THR A 742 " pdb=" N THR A 742 " pdb=" C THR A 742 " pdb=" CB THR A 742 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA THR B 742 " pdb=" N THR B 742 " pdb=" C THR B 742 " pdb=" CB THR B 742 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CA VAL A 28 " pdb=" N VAL A 28 " pdb=" C VAL A 28 " pdb=" CB VAL A 28 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 2064 not shown) Planarity restraints: 2358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 307 " 0.019 2.00e-02 2.50e+03 1.53e-02 5.81e+00 pdb=" CG TRP A 307 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 307 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 307 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 307 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 307 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 307 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 307 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 307 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 307 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP C 107 " 0.036 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO C 108 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 108 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 108 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 107 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO D 108 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 108 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 108 " -0.027 5.00e-02 4.00e+02 ... (remaining 2355 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1735 2.75 - 3.29: 12669 3.29 - 3.83: 21169 3.83 - 4.36: 23105 4.36 - 4.90: 41560 Nonbonded interactions: 100238 Sorted by model distance: nonbonded pdb=" O SER B 116 " pdb=" OG SER B 120 " model vdw 2.217 2.440 nonbonded pdb=" O TYR A 629 " pdb=" OG1 THR A 632 " model vdw 2.219 2.440 nonbonded pdb=" O TYR B 629 " pdb=" OG1 THR B 632 " model vdw 2.225 2.440 nonbonded pdb=" OH TYR B 311 " pdb=" OD1 ASP B 480 " model vdw 2.254 2.440 nonbonded pdb=" OH TYR A 311 " pdb=" OD1 ASP A 480 " model vdw 2.257 2.440 ... (remaining 100233 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 538 or (resid 539 and (name N or name CA or nam \ e C or name O or name CB )) or resid 540 through 827 or resid 901)) selection = (chain 'B' and (resid 25 through 258 or (resid 259 and (name N or name CA or nam \ e C or name O or name CB )) or resid 260 through 540 or (resid 541 and (name N o \ r name CA or name C or name O or name CB )) or resid 542 through 827 or resid 90 \ 1)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 3 through 92 or (resid 93 through 94 and (name N or name C \ A or name C or name O or name CB )) or resid 95 through 125)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 38.870 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 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 : 0.003 0.073 13388 Z= 0.230 Angle : 0.624 13.304 18243 Z= 0.315 Chirality : 0.044 0.163 2067 Planarity : 0.004 0.055 2358 Dihedral : 13.359 89.659 4563 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.21), residues: 1778 helix: 1.80 (0.20), residues: 700 sheet: -0.69 (0.31), residues: 298 loop : -0.90 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 307 HIS 0.005 0.001 HIS A 45 PHE 0.017 0.001 PHE B 456 TYR 0.016 0.001 TYR D 103 ARG 0.008 0.001 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.485 Fit side-chains REVERT: B 307 TRP cc_start: 0.6663 (p-90) cc_final: 0.5934 (p-90) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2713 time to fit residues: 67.6869 Evaluate side-chains 152 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 91 optimal weight: 0.0970 chunk 72 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 53 optimal weight: 0.1980 chunk 84 optimal weight: 0.5980 chunk 103 optimal weight: 0.4980 chunk 161 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.0686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13388 Z= 0.177 Angle : 0.561 12.236 18243 Z= 0.282 Chirality : 0.043 0.221 2067 Planarity : 0.004 0.049 2358 Dihedral : 4.536 47.006 1940 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.55 % Allowed : 6.57 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1778 helix: 1.79 (0.20), residues: 724 sheet: -0.84 (0.29), residues: 326 loop : -0.78 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 307 HIS 0.003 0.001 HIS A 218 PHE 0.029 0.002 PHE A 712 TYR 0.012 0.001 TYR B 481 ARG 0.007 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 161 time to evaluate : 1.401 Fit side-chains REVERT: B 307 TRP cc_start: 0.6606 (p-90) cc_final: 0.5931 (p-90) outliers start: 7 outliers final: 5 residues processed: 162 average time/residue: 0.2834 time to fit residues: 64.8056 Evaluate side-chains 157 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain D residue 32 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 110 optimal weight: 0.0470 chunk 44 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 174 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 55 optimal weight: 30.0000 chunk 129 optimal weight: 0.9980 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN C 41 GLN C 84 GLN D 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13388 Z= 0.261 Angle : 0.580 10.542 18243 Z= 0.293 Chirality : 0.044 0.204 2067 Planarity : 0.004 0.048 2358 Dihedral : 4.564 48.164 1940 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.87 % Allowed : 9.89 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1778 helix: 1.86 (0.20), residues: 726 sheet: -0.88 (0.29), residues: 324 loop : -0.86 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 307 HIS 0.005 0.001 HIS A 44 PHE 0.027 0.002 PHE A 712 TYR 0.016 0.001 TYR A 547 ARG 0.008 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 164 time to evaluate : 1.496 Fit side-chains revert: symmetry clash REVERT: B 307 TRP cc_start: 0.6833 (p-90) cc_final: 0.6424 (p-90) REVERT: D 103 TYR cc_start: 0.7365 (m-80) cc_final: 0.7071 (m-80) outliers start: 11 outliers final: 9 residues processed: 168 average time/residue: 0.2829 time to fit residues: 68.3898 Evaluate side-chains 167 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 158 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 9.9990 chunk 121 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 162 optimal weight: 9.9990 chunk 172 optimal weight: 8.9990 chunk 154 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 13388 Z= 0.415 Angle : 0.666 11.584 18243 Z= 0.338 Chirality : 0.047 0.211 2067 Planarity : 0.005 0.049 2358 Dihedral : 4.877 49.961 1940 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.42 % Allowed : 14.48 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1778 helix: 1.78 (0.20), residues: 726 sheet: -0.95 (0.31), residues: 300 loop : -1.06 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 307 HIS 0.009 0.001 HIS A 44 PHE 0.035 0.002 PHE B 456 TYR 0.020 0.002 TYR A 547 ARG 0.007 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 1.599 Fit side-chains revert: symmetry clash REVERT: B 307 TRP cc_start: 0.7046 (p-90) cc_final: 0.6532 (p-90) outliers start: 18 outliers final: 13 residues processed: 172 average time/residue: 0.2659 time to fit residues: 65.5610 Evaluate side-chains 170 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 157 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 735 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 154 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN D 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13388 Z= 0.290 Angle : 0.606 11.580 18243 Z= 0.305 Chirality : 0.045 0.276 2067 Planarity : 0.004 0.048 2358 Dihedral : 4.762 48.958 1940 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.37 % Allowed : 15.59 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1778 helix: 1.76 (0.20), residues: 728 sheet: -0.92 (0.30), residues: 320 loop : -1.01 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 307 HIS 0.007 0.001 HIS B 44 PHE 0.025 0.002 PHE B 456 TYR 0.017 0.001 TYR B 481 ARG 0.009 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 1.434 Fit side-chains revert: symmetry clash REVERT: A 360 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8145 (mt0) REVERT: A 414 MET cc_start: 0.7977 (tmm) cc_final: 0.7740 (tmm) REVERT: B 360 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8152 (mt0) outliers start: 30 outliers final: 19 residues processed: 182 average time/residue: 0.2643 time to fit residues: 68.8090 Evaluate side-chains 179 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 735 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 172 optimal weight: 0.0040 chunk 142 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN D 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13388 Z= 0.269 Angle : 0.603 12.065 18243 Z= 0.302 Chirality : 0.046 0.397 2067 Planarity : 0.004 0.048 2358 Dihedral : 4.714 48.075 1940 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.69 % Allowed : 16.14 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1778 helix: 1.74 (0.20), residues: 730 sheet: -0.88 (0.30), residues: 320 loop : -0.98 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 307 HIS 0.005 0.001 HIS A 44 PHE 0.024 0.002 PHE B 456 TYR 0.017 0.001 TYR B 481 ARG 0.009 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 160 time to evaluate : 1.310 Fit side-chains revert: symmetry clash REVERT: B 414 MET cc_start: 0.8001 (tmm) cc_final: 0.7715 (tmm) outliers start: 34 outliers final: 29 residues processed: 183 average time/residue: 0.2632 time to fit residues: 69.1160 Evaluate side-chains 187 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 735 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 144 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 chunk 171 optimal weight: 7.9990 chunk 107 optimal weight: 0.2980 chunk 104 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13388 Z= 0.204 Angle : 0.577 12.216 18243 Z= 0.288 Chirality : 0.044 0.368 2067 Planarity : 0.004 0.048 2358 Dihedral : 4.588 47.378 1940 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.29 % Allowed : 17.33 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.21), residues: 1778 helix: 1.76 (0.20), residues: 730 sheet: -0.83 (0.30), residues: 320 loop : -0.93 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 307 HIS 0.004 0.001 HIS A 44 PHE 0.021 0.002 PHE A 712 TYR 0.019 0.001 TYR A 542 ARG 0.009 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 1.491 Fit side-chains revert: symmetry clash REVERT: B 307 TRP cc_start: 0.6794 (p-90) cc_final: 0.6118 (p-90) REVERT: B 414 MET cc_start: 0.7947 (tmm) cc_final: 0.7731 (tmm) outliers start: 29 outliers final: 27 residues processed: 180 average time/residue: 0.2574 time to fit residues: 66.6239 Evaluate side-chains 187 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 735 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 chunk 109 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 164 optimal weight: 0.6980 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13388 Z= 0.329 Angle : 0.634 11.872 18243 Z= 0.318 Chirality : 0.047 0.388 2067 Planarity : 0.004 0.047 2358 Dihedral : 4.761 48.773 1940 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.01 % Allowed : 17.41 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1778 helix: 1.70 (0.20), residues: 736 sheet: -1.03 (0.30), residues: 298 loop : -0.96 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 307 HIS 0.006 0.001 HIS A 44 PHE 0.030 0.002 PHE B 456 TYR 0.018 0.002 TYR A 547 ARG 0.009 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 156 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: B 307 TRP cc_start: 0.6977 (p-90) cc_final: 0.6267 (p-90) outliers start: 38 outliers final: 35 residues processed: 182 average time/residue: 0.2634 time to fit residues: 68.8028 Evaluate side-chains 190 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 155 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 531 CYS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 735 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 96 optimal weight: 0.4980 chunk 69 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 104 optimal weight: 0.3980 chunk 169 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13388 Z= 0.188 Angle : 0.583 11.963 18243 Z= 0.289 Chirality : 0.045 0.375 2067 Planarity : 0.004 0.048 2358 Dihedral : 4.562 47.718 1940 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.37 % Allowed : 18.35 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.21), residues: 1778 helix: 1.77 (0.20), residues: 728 sheet: -0.92 (0.31), residues: 298 loop : -0.89 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 307 HIS 0.004 0.001 HIS B 218 PHE 0.018 0.001 PHE A 712 TYR 0.016 0.001 TYR A 547 ARG 0.010 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 165 time to evaluate : 1.317 Fit side-chains revert: symmetry clash REVERT: B 307 TRP cc_start: 0.6765 (p-90) cc_final: 0.6017 (p-90) REVERT: C 103 TYR cc_start: 0.7529 (m-80) cc_final: 0.6941 (m-80) outliers start: 30 outliers final: 26 residues processed: 185 average time/residue: 0.2629 time to fit residues: 69.8542 Evaluate side-chains 186 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 160 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 735 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 177 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13388 Z= 0.340 Angle : 0.647 12.257 18243 Z= 0.325 Chirality : 0.047 0.400 2067 Planarity : 0.004 0.048 2358 Dihedral : 4.762 48.804 1940 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.37 % Allowed : 18.91 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1778 helix: 1.70 (0.20), residues: 734 sheet: -1.00 (0.30), residues: 298 loop : -0.93 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 307 HIS 0.006 0.001 HIS A 44 PHE 0.031 0.002 PHE B 456 TYR 0.017 0.002 TYR B 481 ARG 0.010 0.001 ARG A 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 154 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: B 307 TRP cc_start: 0.6994 (p-90) cc_final: 0.6260 (p-90) outliers start: 30 outliers final: 30 residues processed: 176 average time/residue: 0.2624 time to fit residues: 66.3146 Evaluate side-chains 182 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 531 CYS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 735 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 145 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** 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 = 0.4351 r_free = 0.4351 target = 0.142443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3747 r_free = 0.3747 target = 0.106759 restraints weight = 29801.373| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.98 r_work: 0.3610 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13388 Z= 0.245 Angle : 0.610 13.258 18243 Z= 0.304 Chirality : 0.046 0.406 2067 Planarity : 0.004 0.048 2358 Dihedral : 4.652 48.010 1940 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.29 % Allowed : 19.22 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.21), residues: 1778 helix: 1.76 (0.20), residues: 728 sheet: -0.94 (0.31), residues: 298 loop : -0.93 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 307 HIS 0.005 0.001 HIS A 44 PHE 0.022 0.002 PHE B 456 TYR 0.017 0.001 TYR B 792 ARG 0.010 0.001 ARG B 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2844.69 seconds wall clock time: 51 minutes 12.29 seconds (3072.29 seconds total)