Starting phenix.real_space_refine on Thu Jan 18 22:33:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nf7_12297/01_2024/7nf7_12297.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nf7_12297/01_2024/7nf7_12297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nf7_12297/01_2024/7nf7_12297.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nf7_12297/01_2024/7nf7_12297.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nf7_12297/01_2024/7nf7_12297.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nf7_12297/01_2024/7nf7_12297.pdb" } resolution = 2.68 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= 0.003 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 46 5.16 5 C 6114 2.51 5 N 1624 2.21 5 O 1856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 147": "OD1" <-> "OD2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A ASP 359": "OD1" <-> "OD2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A GLU 496": "OE1" <-> "OE2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 539": "OD1" <-> "OD2" Residue "A ARG 546": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "A ASP 587": "OD1" <-> "OD2" Residue "A ARG 617": "NH1" <-> "NH2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 631": "NH1" <-> "NH2" Residue "A ASP 634": "OD1" <-> "OD2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A ARG 665": "NH1" <-> "NH2" Residue "A PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 147": "OD1" <-> "OD2" Residue "D ASP 150": "OD1" <-> "OD2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ASP 202": "OD1" <-> "OD2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D ARG 270": "NH1" <-> "NH2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "D ASP 338": "OD1" <-> "OD2" Residue "D ASP 359": "OD1" <-> "OD2" Residue "D ARG 362": "NH1" <-> "NH2" Residue "D ARG 365": "NH1" <-> "NH2" Residue "D GLU 374": "OE1" <-> "OE2" Residue "D ARG 377": "NH1" <-> "NH2" Residue "D GLU 388": "OE1" <-> "OE2" Residue "D GLU 392": "OE1" <-> "OE2" Residue "D GLU 433": "OE1" <-> "OE2" Residue "D GLU 437": "OE1" <-> "OE2" Residue "D ARG 452": "NH1" <-> "NH2" Residue "D GLU 496": "OE1" <-> "OE2" Residue "D ASP 499": "OD1" <-> "OD2" Residue "D PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 539": "OD1" <-> "OD2" Residue "D ARG 546": "NH1" <-> "NH2" Residue "D GLU 554": "OE1" <-> "OE2" Residue "D GLU 562": "OE1" <-> "OE2" Residue "D ARG 574": "NH1" <-> "NH2" Residue "D ARG 584": "NH1" <-> "NH2" Residue "D GLU 585": "OE1" <-> "OE2" Residue "D ASP 587": "OD1" <-> "OD2" Residue "D ARG 617": "NH1" <-> "NH2" Residue "D ARG 619": "NH1" <-> "NH2" Residue "D TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 631": "NH1" <-> "NH2" Residue "D ASP 634": "OD1" <-> "OD2" Residue "D GLU 649": "OE1" <-> "OE2" Residue "D ARG 665": "NH1" <-> "NH2" Residue "D PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9642 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4708 Classifications: {'peptide': 575} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 551} Chain: "B" 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: "C" 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: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 4708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4708 Classifications: {'peptide': 575} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 551} Chain: "E" 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: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.48, per 1000 atoms: 0.57 Number of scatterers: 9642 At special positions: 0 Unit cell: (130.729, 121.94, 90.0819, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 46 16.00 O 1856 8.00 N 1624 7.00 C 6114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 666 " distance=2.04 Simple disulfide: pdb=" SG CYS A 673 " - pdb=" SG CYS A 685 " distance=2.03 Simple disulfide: pdb=" SG CYS D 242 " - pdb=" SG CYS D 273 " distance=2.03 Simple disulfide: pdb=" SG CYS D 571 " - pdb=" SG CYS D 666 " distance=2.04 Simple disulfide: pdb=" SG CYS D 673 " - pdb=" SG CYS D 685 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 702 " - " ASN A 513 " " NAG A 703 " - " ASN A 246 " " NAG A 704 " - " ASN A 228 " " NAG A 705 " - " ASN A 523 " " NAG B 1 " - " ASN A 332 " " NAG C 1 " - " ASN A 261 " " NAG D 702 " - " ASN D 513 " " NAG D 703 " - " ASN D 246 " " NAG D 704 " - " ASN D 228 " " NAG D 705 " - " ASN D 523 " " NAG E 1 " - " ASN D 332 " " NAG F 1 " - " ASN D 261 " Time building additional restraints: 3.80 Conformation dependent library (CDL) restraints added in 1.8 seconds 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 16 sheets defined 35.8% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 116 through 121 removed outlier: 3.909A pdb=" N GLY A 121 " --> pdb=" O TRP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.759A pdb=" N PHE A 131 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 removed outlier: 3.573A pdb=" N LYS A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.501A pdb=" N ILE A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 189 through 203 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.610A pdb=" N THR A 234 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP A 235 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 removed outlier: 3.838A pdb=" N GLN A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 319 removed outlier: 3.684A pdb=" N TYR A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.779A pdb=" N VAL A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.785A pdb=" N ILE A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 396 removed outlier: 3.521A pdb=" N VAL A 395 " --> pdb=" O GLU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 435 removed outlier: 3.501A pdb=" N VAL A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.984A pdb=" N SER A 505 " --> pdb=" O THR A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 530 through 535 removed outlier: 4.389A pdb=" N HIS A 534 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 547 through 561 Processing helix chain 'A' and resid 587 through 590 removed outlier: 4.050A pdb=" N ASN A 590 " --> pdb=" O ASP A 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 587 through 590' Processing helix chain 'A' and resid 606 through 612 removed outlier: 3.892A pdb=" N MET A 610 " --> pdb=" O ASN A 606 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'D' and resid 116 through 121 removed outlier: 3.909A pdb=" N GLY D 121 " --> pdb=" O TRP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 3.759A pdb=" N PHE D 131 " --> pdb=" O PRO D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 148 removed outlier: 3.573A pdb=" N LYS D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 155 removed outlier: 3.501A pdb=" N ILE D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 155 " --> pdb=" O TYR D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 188 Processing helix chain 'D' and resid 189 through 203 Processing helix chain 'D' and resid 220 through 227 Processing helix chain 'D' and resid 230 through 236 removed outlier: 3.610A pdb=" N THR D 234 " --> pdb=" O GLY D 231 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP D 235 " --> pdb=" O LYS D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 306 removed outlier: 3.838A pdb=" N GLN D 293 " --> pdb=" O ASN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 319 removed outlier: 3.684A pdb=" N TYR D 318 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 340 removed outlier: 3.779A pdb=" N VAL D 340 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 344 No H-bonds generated for 'chain 'D' and resid 342 through 344' Processing helix chain 'D' and resid 356 through 370 removed outlier: 3.785A pdb=" N ILE D 360 " --> pdb=" O GLY D 356 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN D 370 " --> pdb=" O GLN D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 396 removed outlier: 3.521A pdb=" N VAL D 395 " --> pdb=" O GLU D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 435 removed outlier: 3.501A pdb=" N VAL D 427 " --> pdb=" O SER D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 457 Processing helix chain 'D' and resid 458 through 460 No H-bonds generated for 'chain 'D' and resid 458 through 460' Processing helix chain 'D' and resid 461 through 472 Processing helix chain 'D' and resid 481 through 485 Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.984A pdb=" N SER D 505 " --> pdb=" O THR D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 519 Processing helix chain 'D' and resid 530 through 535 removed outlier: 4.389A pdb=" N HIS D 534 " --> pdb=" O SER D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 547 through 561 Processing helix chain 'D' and resid 587 through 590 removed outlier: 4.050A pdb=" N ASN D 590 " --> pdb=" O ASP D 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 587 through 590' Processing helix chain 'D' and resid 606 through 612 removed outlier: 3.892A pdb=" N MET D 610 " --> pdb=" O ASN D 606 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER D 612 " --> pdb=" O LYS D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 664 No H-bonds generated for 'chain 'D' and resid 662 through 664' Processing sheet with id= 1, first strand: chain 'A' and resid 407 through 409 removed outlier: 6.697A pdb=" N MET A 381 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N PHE A 409 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR A 383 " --> pdb=" O PHE A 409 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY A 310 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP A 443 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N TYR A 479 " --> pdb=" O TRP A 443 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 166 through 170 removed outlier: 7.038A pdb=" N LYS A 167 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA A 176 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.606A pdb=" N GLN A 272 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 243 through 245 removed outlier: 3.912A pdb=" N ASN A 243 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 329 through 330 removed outlier: 4.165A pdb=" N ALA A 329 " --> pdb=" O HIS A 347 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 632 through 634 removed outlier: 3.506A pdb=" N ARG A 619 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 647 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A 623 " --> pdb=" O GLY A 645 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY A 645 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 603 through 605 Processing sheet with id= 8, first strand: chain 'A' and resid 673 through 674 Processing sheet with id= 9, first strand: chain 'D' and resid 407 through 409 removed outlier: 6.697A pdb=" N MET D 381 " --> pdb=" O PHE D 407 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N PHE D 409 " --> pdb=" O MET D 381 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR D 383 " --> pdb=" O PHE D 409 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY D 310 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP D 443 " --> pdb=" O ILE D 477 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N TYR D 479 " --> pdb=" O TRP D 443 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 166 through 170 removed outlier: 7.038A pdb=" N LYS D 167 " --> pdb=" O GLU D 178 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA D 176 " --> pdb=" O SER D 169 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 239 through 240 removed outlier: 3.606A pdb=" N GLN D 272 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 243 through 245 removed outlier: 3.912A pdb=" N ASN D 243 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 329 through 330 removed outlier: 4.165A pdb=" N ALA D 329 " --> pdb=" O HIS D 347 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 632 through 634 removed outlier: 3.506A pdb=" N ARG D 619 " --> pdb=" O GLU D 649 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE D 647 " --> pdb=" O ARG D 621 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER D 623 " --> pdb=" O GLY D 645 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY D 645 " --> pdb=" O SER D 623 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 603 through 605 Processing sheet with id= 16, first strand: chain 'D' and resid 673 through 674 298 hydrogen bonds defined for protein. 756 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: 3.21 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2996 1.33 - 1.45: 1804 1.45 - 1.57: 5020 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 9898 Sorted by residual: bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 NAG D 703 " pdb=" O5 NAG D 703 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C1 NAG D 704 " pdb=" O5 NAG D 704 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.70e+00 ... (remaining 9893 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.37: 258 106.37 - 113.28: 5338 113.28 - 120.19: 3520 120.19 - 127.10: 4170 127.10 - 134.00: 148 Bond angle restraints: 13434 Sorted by residual: angle pdb=" C PHE A 173 " pdb=" N ARG A 174 " pdb=" CA ARG A 174 " ideal model delta sigma weight residual 121.54 128.52 -6.98 1.91e+00 2.74e-01 1.34e+01 angle pdb=" C PHE D 173 " pdb=" N ARG D 174 " pdb=" CA ARG D 174 " ideal model delta sigma weight residual 121.54 128.52 -6.98 1.91e+00 2.74e-01 1.34e+01 angle pdb=" CA PHE D 173 " pdb=" C PHE D 173 " pdb=" N ARG D 174 " ideal model delta sigma weight residual 116.21 111.96 4.25 1.29e+00 6.01e-01 1.08e+01 angle pdb=" CA PHE A 173 " pdb=" C PHE A 173 " pdb=" N ARG A 174 " ideal model delta sigma weight residual 116.21 111.96 4.25 1.29e+00 6.01e-01 1.08e+01 angle pdb=" C GLU D 562 " pdb=" N LEU D 563 " pdb=" CA LEU D 563 " ideal model delta sigma weight residual 121.54 127.14 -5.60 1.91e+00 2.74e-01 8.61e+00 ... (remaining 13429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5224 17.99 - 35.97: 580 35.97 - 53.96: 176 53.96 - 71.95: 44 71.95 - 89.94: 16 Dihedral angle restraints: 6040 sinusoidal: 2670 harmonic: 3370 Sorted by residual: dihedral pdb=" CA ARG D 174 " pdb=" C ARG D 174 " pdb=" N HIS D 175 " pdb=" CA HIS D 175 " ideal model delta harmonic sigma weight residual 180.00 135.39 44.61 0 5.00e+00 4.00e-02 7.96e+01 dihedral pdb=" CA ARG A 174 " pdb=" C ARG A 174 " pdb=" N HIS A 175 " pdb=" CA HIS A 175 " ideal model delta harmonic sigma weight residual 180.00 135.39 44.61 0 5.00e+00 4.00e-02 7.96e+01 dihedral pdb=" CA ASN A 575 " pdb=" C ASN A 575 " pdb=" N ASP A 576 " pdb=" CA ASP A 576 " ideal model delta harmonic sigma weight residual 180.00 155.06 24.94 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 6037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1172 0.057 - 0.114: 266 0.114 - 0.171: 18 0.171 - 0.228: 4 0.228 - 0.285: 2 Chirality restraints: 1462 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 1.03e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 1.03e+01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 513 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1459 not shown) Planarity restraints: 1726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 513 " 0.036 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN A 513 " 0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN A 513 " -0.285 2.00e-02 2.50e+03 pdb=" ND2 ASN A 513 " 0.553 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " -0.388 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 513 " -0.036 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN D 513 " -0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN D 513 " 0.285 2.00e-02 2.50e+03 pdb=" ND2 ASN D 513 " -0.553 2.00e-02 2.50e+03 pdb=" C1 NAG D 702 " 0.388 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 246 " 0.090 2.00e-02 2.50e+03 3.22e-01 1.30e+03 pdb=" CG ASN D 246 " -0.088 2.00e-02 2.50e+03 pdb=" OD1 ASN D 246 " 0.195 2.00e-02 2.50e+03 pdb=" ND2 ASN D 246 " -0.571 2.00e-02 2.50e+03 pdb=" C1 NAG D 703 " 0.374 2.00e-02 2.50e+03 ... (remaining 1723 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3358 2.85 - 3.36: 8349 3.36 - 3.87: 16324 3.87 - 4.39: 20480 4.39 - 4.90: 33221 Nonbonded interactions: 81732 Sorted by model distance: nonbonded pdb=" OG SER A 226 " pdb=" O TYR A 233 " model vdw 2.336 2.440 nonbonded pdb=" OG SER D 226 " pdb=" O TYR D 233 " model vdw 2.336 2.440 nonbonded pdb=" NH1 ARG A 574 " pdb=" OD1 ASP A 576 " model vdw 2.349 2.520 nonbonded pdb=" NH1 ARG D 574 " pdb=" OD1 ASP D 576 " model vdw 2.349 2.520 nonbonded pdb=" OH TYR D 151 " pdb=" OE2 GLU D 483 " model vdw 2.365 2.440 ... (remaining 81727 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' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'F' } 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: 2.590 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: 6.870 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 28.120 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 : 0.006 0.037 9898 Z= 0.374 Angle : 0.711 11.217 13434 Z= 0.400 Chirality : 0.048 0.285 1462 Planarity : 0.005 0.055 1714 Dihedral : 17.227 89.937 3858 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.71 % Favored : 95.11 % Rotamer: Outliers : 6.53 % Allowed : 18.43 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.11 (0.21), residues: 1146 helix: -3.42 (0.18), residues: 272 sheet: -1.83 (0.34), residues: 186 loop : -1.53 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 443 HIS 0.006 0.001 HIS D 348 PHE 0.019 0.002 PHE A 278 TYR 0.019 0.002 TYR A 259 ARG 0.004 0.001 ARG A 574 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 171 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 MET cc_start: 0.8098 (mmm) cc_final: 0.7795 (mmt) REVERT: A 546 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6311 (ptp-110) REVERT: A 589 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7320 (mp) REVERT: A 590 ASN cc_start: 0.6512 (t0) cc_final: 0.6274 (p0) REVERT: A 613 ASN cc_start: 0.6707 (t0) cc_final: 0.6223 (t0) REVERT: A 619 ARG cc_start: 0.7427 (ttm110) cc_final: 0.7210 (ttm110) REVERT: A 621 ARG cc_start: 0.8216 (tpt90) cc_final: 0.7701 (tpt-90) REVERT: A 634 ASP cc_start: 0.7425 (p0) cc_final: 0.7202 (t0) REVERT: D 279 MET cc_start: 0.8099 (mmm) cc_final: 0.7795 (mmt) REVERT: D 546 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6312 (ptp-110) REVERT: D 589 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7320 (mp) REVERT: D 590 ASN cc_start: 0.6513 (t0) cc_final: 0.6277 (p0) REVERT: D 613 ASN cc_start: 0.6715 (t0) cc_final: 0.6236 (t0) REVERT: D 619 ARG cc_start: 0.7427 (ttm110) cc_final: 0.7211 (ttm110) REVERT: D 621 ARG cc_start: 0.8220 (tpt90) cc_final: 0.7702 (tpt-90) REVERT: D 634 ASP cc_start: 0.7427 (p0) cc_final: 0.7200 (t0) outliers start: 68 outliers final: 44 residues processed: 225 average time/residue: 1.1908 time to fit residues: 286.8033 Evaluate side-chains 203 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 155 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 562 GLU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 601 GLU Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain D residue 664 ASP Chi-restraints excluded: chain D residue 677 VAL Chi-restraints excluded: chain D residue 680 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 0.4980 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 146 GLN A 181 GLN A 201 HIS A 220 HIS A 243 ASN A 282 GLN A 301 GLN A 335 GLN A 345 GLN A 370 GLN A 422 ASN A 434 ASN A 442 ASN A 463 ASN A 466 ASN A 497 ASN A 510 GLN A 561 ASN A 590 ASN A 606 ASN D 146 GLN D 181 GLN D 201 HIS D 220 HIS D 243 ASN D 282 GLN D 301 GLN D 335 GLN D 345 GLN D 366 GLN D 370 GLN D 422 ASN D 434 ASN D 442 ASN D 463 ASN D 466 ASN D 497 ASN D 561 ASN D 606 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9898 Z= 0.220 Angle : 0.679 10.988 13434 Z= 0.343 Chirality : 0.052 0.474 1462 Planarity : 0.005 0.048 1714 Dihedral : 11.031 82.637 1688 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.84 % Favored : 95.99 % Rotamer: Outliers : 4.61 % Allowed : 20.54 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.66 (0.24), residues: 1146 helix: -0.90 (0.28), residues: 304 sheet: -1.64 (0.34), residues: 214 loop : -0.91 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 443 HIS 0.006 0.001 HIS A 175 PHE 0.014 0.002 PHE A 278 TYR 0.016 0.002 TYR A 259 ARG 0.002 0.000 ARG D 229 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 168 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.7577 (t70) cc_final: 0.7136 (t70) REVERT: A 279 MET cc_start: 0.7972 (mmm) cc_final: 0.7624 (mmt) REVERT: A 589 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7346 (mp) REVERT: A 613 ASN cc_start: 0.6560 (t0) cc_final: 0.6110 (t0) REVERT: A 616 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7407 (m) REVERT: A 621 ARG cc_start: 0.8226 (tpt90) cc_final: 0.7734 (tpt-90) REVERT: A 634 ASP cc_start: 0.7422 (p0) cc_final: 0.7125 (t0) REVERT: D 279 MET cc_start: 0.7975 (mmm) cc_final: 0.7627 (mmt) REVERT: D 298 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7291 (mt-10) REVERT: D 589 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7348 (mp) REVERT: D 613 ASN cc_start: 0.6565 (t0) cc_final: 0.6119 (t0) REVERT: D 616 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7408 (m) REVERT: D 621 ARG cc_start: 0.8226 (tpt90) cc_final: 0.7732 (tpt-90) REVERT: D 634 ASP cc_start: 0.7419 (p0) cc_final: 0.7124 (t0) outliers start: 48 outliers final: 27 residues processed: 204 average time/residue: 1.0970 time to fit residues: 241.7468 Evaluate side-chains 187 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 601 GLU Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 680 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 0.0040 chunk 86 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 GLN A 561 ASN D 301 GLN D 561 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9898 Z= 0.194 Angle : 0.615 10.200 13434 Z= 0.317 Chirality : 0.048 0.394 1462 Planarity : 0.004 0.044 1714 Dihedral : 9.459 79.458 1644 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.19 % Favored : 95.64 % Rotamer: Outliers : 4.80 % Allowed : 20.92 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.07 (0.25), residues: 1146 helix: 0.08 (0.31), residues: 292 sheet: -1.51 (0.34), residues: 214 loop : -0.71 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 443 HIS 0.005 0.001 HIS A 175 PHE 0.013 0.001 PHE D 407 TYR 0.016 0.001 TYR D 259 ARG 0.002 0.000 ARG D 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 157 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.7483 (t70) cc_final: 0.7236 (m90) REVERT: A 250 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8224 (mm) REVERT: A 279 MET cc_start: 0.7970 (mmm) cc_final: 0.7623 (mmt) REVERT: A 280 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8495 (pttm) REVERT: A 336 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7979 (mt) REVERT: A 377 ARG cc_start: 0.8225 (mtp180) cc_final: 0.8023 (mtp180) REVERT: A 423 SER cc_start: 0.8159 (t) cc_final: 0.7845 (m) REVERT: A 546 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6185 (ptp-110) REVERT: A 613 ASN cc_start: 0.6558 (t0) cc_final: 0.6142 (t0) REVERT: A 616 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.7502 (m) REVERT: A 621 ARG cc_start: 0.8186 (tpt90) cc_final: 0.7754 (tpt-90) REVERT: A 634 ASP cc_start: 0.7429 (p0) cc_final: 0.7174 (t70) REVERT: D 250 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8220 (mm) REVERT: D 279 MET cc_start: 0.7973 (mmm) cc_final: 0.7628 (mmt) REVERT: D 280 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8490 (pttm) REVERT: D 298 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7094 (mt-10) REVERT: D 336 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7982 (mt) REVERT: D 377 ARG cc_start: 0.8227 (mtp180) cc_final: 0.8025 (mtp180) REVERT: D 423 SER cc_start: 0.8160 (t) cc_final: 0.7846 (m) REVERT: D 546 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6190 (ptp-110) REVERT: D 613 ASN cc_start: 0.6559 (t0) cc_final: 0.6150 (t0) REVERT: D 616 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7503 (m) REVERT: D 621 ARG cc_start: 0.8189 (tpt90) cc_final: 0.7755 (tpt-90) REVERT: D 634 ASP cc_start: 0.7425 (p0) cc_final: 0.7171 (t70) outliers start: 50 outliers final: 27 residues processed: 196 average time/residue: 1.1977 time to fit residues: 252.1298 Evaluate side-chains 189 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 151 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 680 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 110 optimal weight: 0.0670 chunk 54 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 GLN A 366 GLN D 301 GLN D 516 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9898 Z= 0.162 Angle : 0.587 10.593 13434 Z= 0.301 Chirality : 0.047 0.357 1462 Planarity : 0.004 0.042 1714 Dihedral : 8.397 74.908 1630 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.19 % Favored : 95.64 % Rotamer: Outliers : 4.41 % Allowed : 21.11 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.87 (0.25), residues: 1146 helix: 0.37 (0.32), residues: 294 sheet: -1.38 (0.34), residues: 212 loop : -0.67 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 443 HIS 0.006 0.001 HIS A 175 PHE 0.011 0.001 PHE A 278 TYR 0.014 0.001 TYR D 259 ARG 0.001 0.000 ARG D 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 153 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.7489 (t70) cc_final: 0.7244 (m90) REVERT: A 279 MET cc_start: 0.7898 (mmm) cc_final: 0.7620 (mmt) REVERT: A 336 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7915 (mt) REVERT: A 423 SER cc_start: 0.8231 (t) cc_final: 0.8016 (m) REVERT: A 509 MET cc_start: 0.9008 (tpt) cc_final: 0.8693 (tpt) REVERT: A 546 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6313 (ptp-110) REVERT: A 605 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7957 (pt) REVERT: A 613 ASN cc_start: 0.6744 (t0) cc_final: 0.6313 (t0) REVERT: A 621 ARG cc_start: 0.8100 (tpt90) cc_final: 0.7769 (tpt-90) REVERT: A 634 ASP cc_start: 0.7386 (p0) cc_final: 0.7166 (t70) REVERT: D 279 MET cc_start: 0.7901 (mmm) cc_final: 0.7624 (mmt) REVERT: D 336 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7919 (mt) REVERT: D 423 SER cc_start: 0.8232 (t) cc_final: 0.8018 (m) REVERT: D 546 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6317 (ptp-110) REVERT: D 605 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7963 (pt) REVERT: D 613 ASN cc_start: 0.6744 (t0) cc_final: 0.6320 (t0) REVERT: D 621 ARG cc_start: 0.8101 (tpt90) cc_final: 0.7766 (tpt-90) REVERT: D 634 ASP cc_start: 0.7387 (p0) cc_final: 0.7164 (t70) outliers start: 46 outliers final: 27 residues processed: 190 average time/residue: 1.2473 time to fit residues: 255.3075 Evaluate side-chains 178 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 145 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 664 ASP Chi-restraints excluded: chain D residue 680 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9898 Z= 0.235 Angle : 0.626 10.034 13434 Z= 0.323 Chirality : 0.049 0.343 1462 Planarity : 0.004 0.043 1714 Dihedral : 8.082 74.836 1626 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.84 % Favored : 95.99 % Rotamer: Outliers : 4.89 % Allowed : 20.63 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.82 (0.25), residues: 1146 helix: 0.39 (0.31), residues: 294 sheet: -1.46 (0.34), residues: 214 loop : -0.57 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 443 HIS 0.006 0.001 HIS D 175 PHE 0.017 0.002 PHE D 407 TYR 0.017 0.001 TYR A 259 ARG 0.003 0.000 ARG D 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 147 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.7500 (t70) cc_final: 0.7249 (m90) REVERT: A 250 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8198 (mm) REVERT: A 279 MET cc_start: 0.7952 (mmm) cc_final: 0.7678 (mmt) REVERT: A 336 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7918 (mt) REVERT: A 423 SER cc_start: 0.8207 (t) cc_final: 0.7970 (m) REVERT: A 453 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8548 (tt) REVERT: A 509 MET cc_start: 0.8990 (tpt) cc_final: 0.8765 (tpt) REVERT: A 546 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.6316 (ptp-110) REVERT: A 613 ASN cc_start: 0.6793 (t0) cc_final: 0.6357 (t0) REVERT: A 616 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7504 (m) REVERT: A 621 ARG cc_start: 0.8106 (tpt90) cc_final: 0.7706 (tpt-90) REVERT: A 634 ASP cc_start: 0.7416 (p0) cc_final: 0.7180 (t70) REVERT: D 250 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8193 (mm) REVERT: D 279 MET cc_start: 0.7953 (mmm) cc_final: 0.7680 (mmt) REVERT: D 298 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7113 (mt-10) REVERT: D 336 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7922 (mt) REVERT: D 423 SER cc_start: 0.8206 (t) cc_final: 0.7971 (m) REVERT: D 453 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8551 (tt) REVERT: D 509 MET cc_start: 0.9056 (tpt) cc_final: 0.8794 (tpt) REVERT: D 546 ARG cc_start: 0.6931 (OUTLIER) cc_final: 0.6320 (ptp-110) REVERT: D 613 ASN cc_start: 0.6793 (t0) cc_final: 0.6366 (t0) REVERT: D 616 THR cc_start: 0.8042 (OUTLIER) cc_final: 0.7508 (m) REVERT: D 621 ARG cc_start: 0.8107 (tpt90) cc_final: 0.7704 (tpt-90) REVERT: D 634 ASP cc_start: 0.7418 (p0) cc_final: 0.7180 (t70) outliers start: 51 outliers final: 30 residues processed: 188 average time/residue: 1.1816 time to fit residues: 238.6974 Evaluate side-chains 184 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 143 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 664 ASP Chi-restraints excluded: chain D residue 680 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.0670 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9898 Z= 0.288 Angle : 0.655 10.185 13434 Z= 0.339 Chirality : 0.050 0.338 1462 Planarity : 0.004 0.043 1714 Dihedral : 8.036 76.645 1626 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.81 % Rotamer: Outliers : 4.32 % Allowed : 21.31 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.25), residues: 1146 helix: 0.24 (0.31), residues: 294 sheet: -0.93 (0.37), residues: 176 loop : -0.65 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 440 HIS 0.006 0.001 HIS A 348 PHE 0.018 0.002 PHE A 407 TYR 0.018 0.002 TYR D 259 ARG 0.003 0.000 ARG D 229 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 150 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 MET cc_start: 0.7960 (mmm) cc_final: 0.7600 (mmt) REVERT: A 423 SER cc_start: 0.8221 (t) cc_final: 0.7944 (m) REVERT: A 453 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8542 (tt) REVERT: A 546 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6393 (ptp-110) REVERT: A 613 ASN cc_start: 0.6871 (t0) cc_final: 0.6443 (t0) REVERT: A 621 ARG cc_start: 0.8142 (tpt90) cc_final: 0.7727 (tpt-90) REVERT: A 634 ASP cc_start: 0.7508 (p0) cc_final: 0.7198 (t70) REVERT: D 250 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8205 (mm) REVERT: D 279 MET cc_start: 0.7960 (mmm) cc_final: 0.7601 (mmt) REVERT: D 298 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: D 423 SER cc_start: 0.8222 (t) cc_final: 0.7949 (m) REVERT: D 453 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8543 (tt) REVERT: D 509 MET cc_start: 0.9027 (tpt) cc_final: 0.8812 (tpt) REVERT: D 546 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6383 (ptp-110) REVERT: D 613 ASN cc_start: 0.6873 (t0) cc_final: 0.6452 (t0) REVERT: D 621 ARG cc_start: 0.8142 (tpt90) cc_final: 0.7725 (tpt-90) REVERT: D 634 ASP cc_start: 0.7509 (p0) cc_final: 0.7197 (t70) outliers start: 45 outliers final: 30 residues processed: 187 average time/residue: 1.1768 time to fit residues: 236.4139 Evaluate side-chains 188 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 152 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 664 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9898 Z= 0.297 Angle : 0.665 9.995 13434 Z= 0.344 Chirality : 0.050 0.336 1462 Planarity : 0.004 0.044 1714 Dihedral : 7.961 78.695 1621 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.10 % Favored : 95.72 % Rotamer: Outliers : 4.70 % Allowed : 21.50 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.77 (0.25), residues: 1146 helix: 0.18 (0.31), residues: 294 sheet: -0.93 (0.36), residues: 176 loop : -0.66 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 443 HIS 0.006 0.001 HIS D 348 PHE 0.017 0.002 PHE D 407 TYR 0.018 0.002 TYR A 259 ARG 0.003 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 153 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 MET cc_start: 0.8042 (mmm) cc_final: 0.7705 (mmt) REVERT: A 453 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8516 (tt) REVERT: A 546 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6675 (ptp90) REVERT: A 613 ASN cc_start: 0.6900 (t0) cc_final: 0.6471 (t0) REVERT: A 621 ARG cc_start: 0.8142 (tpt90) cc_final: 0.7701 (tpt-90) REVERT: A 634 ASP cc_start: 0.7528 (p0) cc_final: 0.7195 (t70) REVERT: D 279 MET cc_start: 0.8042 (mmm) cc_final: 0.7706 (mmt) REVERT: D 298 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7209 (mt-10) REVERT: D 453 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8517 (tt) REVERT: D 546 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6677 (ptp90) REVERT: D 613 ASN cc_start: 0.6907 (t0) cc_final: 0.6482 (t0) REVERT: D 621 ARG cc_start: 0.8143 (tpt90) cc_final: 0.7700 (tpt-90) REVERT: D 634 ASP cc_start: 0.7529 (p0) cc_final: 0.7192 (t70) outliers start: 49 outliers final: 31 residues processed: 192 average time/residue: 1.1989 time to fit residues: 246.8251 Evaluate side-chains 186 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 150 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 556 SER Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 664 ASP Chi-restraints excluded: chain D residue 677 VAL Chi-restraints excluded: chain D residue 680 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.602 > 50: distance: 141 - 146: 29.570 distance: 146 - 147: 19.092 distance: 147 - 148: 55.881 distance: 147 - 150: 39.436 distance: 148 - 149: 51.593 distance: 148 - 155: 54.865 distance: 150 - 151: 3.122 distance: 151 - 152: 36.159 distance: 152 - 153: 42.517 distance: 153 - 154: 53.634 distance: 155 - 156: 38.686 distance: 156 - 157: 15.329 distance: 157 - 158: 21.705 distance: 157 - 164: 43.468 distance: 159 - 160: 39.896 distance: 160 - 161: 20.846 distance: 161 - 162: 60.681 distance: 161 - 163: 22.252 distance: 164 - 165: 65.249 distance: 165 - 166: 41.758 distance: 165 - 168: 44.963 distance: 166 - 167: 21.853 distance: 166 - 173: 68.850 distance: 168 - 169: 25.129 distance: 169 - 170: 10.529 distance: 170 - 171: 49.636 distance: 170 - 172: 26.422 distance: 173 - 174: 40.865 distance: 173 - 179: 57.169 distance: 174 - 175: 49.578 distance: 174 - 177: 43.084 distance: 175 - 176: 40.072 distance: 175 - 180: 63.077 distance: 177 - 178: 21.025 distance: 178 - 179: 56.035 distance: 180 - 181: 69.107 distance: 181 - 182: 56.439 distance: 181 - 184: 54.299 distance: 182 - 188: 56.499 distance: 184 - 185: 30.071 distance: 185 - 186: 40.111 distance: 185 - 187: 48.247 distance: 188 - 189: 39.243 distance: 189 - 190: 40.166 distance: 189 - 192: 70.296 distance: 190 - 196: 55.261 distance: 192 - 193: 61.561 distance: 193 - 194: 59.277 distance: 193 - 195: 49.648 distance: 196 - 197: 52.306 distance: 197 - 198: 12.960 distance: 197 - 200: 13.410 distance: 198 - 199: 28.624 distance: 198 - 204: 57.672 distance: 200 - 201: 50.112 distance: 201 - 202: 22.370 distance: 201 - 203: 39.490 distance: 205 - 206: 39.326 distance: 205 - 208: 14.699 distance: 206 - 207: 45.383 distance: 206 - 215: 40.818 distance: 208 - 209: 45.709 distance: 209 - 210: 29.228 distance: 209 - 211: 31.903 distance: 210 - 212: 62.865 distance: 211 - 213: 40.429 distance: 212 - 214: 11.549 distance: 213 - 214: 30.274 distance: 215 - 216: 56.293 distance: 216 - 217: 57.613 distance: 216 - 219: 39.124 distance: 217 - 226: 39.710 distance: 219 - 220: 5.486 distance: 220 - 221: 22.437 distance: 221 - 222: 18.327 distance: 222 - 223: 16.295 distance: 223 - 224: 11.060 distance: 223 - 225: 4.766 distance: 226 - 227: 57.279 distance: 228 - 234: 35.666 distance: 230 - 231: 56.643 distance: 231 - 232: 41.660 distance: 231 - 233: 41.790