Starting phenix.real_space_refine on Sat Nov 18 03:20:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px8_13691/11_2023/7px8_13691.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px8_13691/11_2023/7px8_13691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px8_13691/11_2023/7px8_13691.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px8_13691/11_2023/7px8_13691.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px8_13691/11_2023/7px8_13691.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px8_13691/11_2023/7px8_13691.pdb" } resolution = 3.27 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: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 13755 2.51 5 N 3683 2.21 5 O 3827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 49": "OE1" <-> "OE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 21409 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5338 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 700, 5279 Classifications: {'peptide': 700} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 653} Chain breaks: 3 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 9, 'GLU:plan': 21, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 159 Conformer: "B" Number of residues, atoms: 700, 5279 Classifications: {'peptide': 700} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 653} Chain breaks: 3 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 9, 'GLU:plan': 21, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 159 bond proxies already assigned to first conformer: 5358 Chain: "B" Number of atoms: 5359 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 700, 5293 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 653} Chain breaks: 3 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 9, 'GLU:plan': 19, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 143 Conformer: "B" Number of residues, atoms: 700, 5293 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 653} Chain breaks: 3 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 9, 'GLU:plan': 19, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 143 bond proxies already assigned to first conformer: 5364 Chain: "C" Number of atoms: 5360 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 699, 5294 Classifications: {'peptide': 699} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 652} Chain breaks: 4 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 18, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 133 Conformer: "B" Number of residues, atoms: 699, 5294 Classifications: {'peptide': 699} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 652} Chain breaks: 4 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 18, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 133 bond proxies already assigned to first conformer: 5364 Chain: "D" Number of atoms: 5352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 699, 5297 Classifications: {'peptide': 699} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 652} Chain breaks: 4 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 18, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 132 Conformer: "B" Number of residues, atoms: 699, 5297 Classifications: {'peptide': 699} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 652} Chain breaks: 4 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 18, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 132 bond proxies already assigned to first conformer: 5379 Residues with excluded nonbonded symmetry interactions: 30 residue: pdb=" N AMET A 584 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 584 " occ=0.50 residue: pdb=" N AGLY A 585 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 585 " occ=0.50 residue: pdb=" N AGLY A 586 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 586 " occ=0.50 residue: pdb=" N ASER A 587 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 587 " occ=0.50 residue: pdb=" N AHIS A 588 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 588 " occ=0.50 residue: pdb=" N AGLY A 589 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 589 " occ=0.50 residue: pdb=" N AGLY A 590 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 590 " occ=0.50 residue: pdb=" N APHE A 591 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 591 " occ=0.50 residue: pdb=" N AMET B 584 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET B 584 " occ=0.50 residue: pdb=" N AGLY B 585 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 585 " occ=0.50 residue: pdb=" N AGLY B 586 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 586 " occ=0.50 residue: pdb=" N ASER B 587 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 587 " occ=0.50 ... (remaining 18 not shown) Time building chain proxies: 20.47, per 1000 atoms: 0.96 Number of scatterers: 21409 At special positions: 0 Unit cell: (135.85, 90.25, 132.05, 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 144 16.00 O 3827 8.00 N 3683 7.00 C 13755 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 7.10 Conformation dependent library (CDL) restraints added in 7.9 seconds 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5216 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 42 sheets defined 19.4% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 9 through 21 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.900A pdb=" N GLU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 139' Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 519 through 527 Processing helix chain 'A' and resid 544 through 549 removed outlier: 3.655A pdb=" N ILE A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 587 through 600 removed outlier: 5.204A pdb=" N BPHE A 591 " --> pdb=" O BSER A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 626 through 634 removed outlier: 3.757A pdb=" N MET A 630 " --> pdb=" O PRO A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 655 Processing helix chain 'A' and resid 680 through 693 Processing helix chain 'A' and resid 711 through 731 removed outlier: 3.635A pdb=" N THR A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS A 729 " --> pdb=" O TRP A 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.965A pdb=" N GLU B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 135 through 139' Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 519 through 527 Processing helix chain 'B' and resid 544 through 551 removed outlier: 3.694A pdb=" N ILE B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 571 Processing helix chain 'B' and resid 587 through 600 removed outlier: 4.988A pdb=" N BPHE B 591 " --> pdb=" O BSER B 587 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS B 595 " --> pdb=" O BPHE B 591 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 598 " --> pdb=" O CYS B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 622 removed outlier: 4.558A pdb=" N GLY B 621 " --> pdb=" O ALA B 617 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER B 622 " --> pdb=" O SER B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 634 removed outlier: 3.864A pdb=" N MET B 630 " --> pdb=" O PRO B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 655 Processing helix chain 'B' and resid 659 through 663 Processing helix chain 'B' and resid 680 through 693 removed outlier: 3.503A pdb=" N ARG B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 730 Processing helix chain 'C' and resid 10 through 21 Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.921A pdb=" N GLU C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 135 through 139' Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 471 through 475 Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 544 through 551 removed outlier: 3.600A pdb=" N ILE C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU C 551 " --> pdb=" O SER C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 572 removed outlier: 3.621A pdb=" N GLN C 572 " --> pdb=" O GLU C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 600 Processing helix chain 'C' and resid 615 through 620 Processing helix chain 'C' and resid 626 through 634 removed outlier: 4.098A pdb=" N MET C 630 " --> pdb=" O PRO C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 654 removed outlier: 3.687A pdb=" N LYS C 654 " --> pdb=" O ALA C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 663 removed outlier: 3.518A pdb=" N TYR C 659 " --> pdb=" O PRO C 656 " (cutoff:3.500A) Proline residue: C 661 - end of helix Processing helix chain 'C' and resid 680 through 693 removed outlier: 3.521A pdb=" N MET C 684 " --> pdb=" O PHE C 680 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG C 693 " --> pdb=" O VAL C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 731 removed outlier: 3.534A pdb=" N SER C 716 " --> pdb=" O VAL C 712 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP C 717 " --> pdb=" O GLU C 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 21 Processing helix chain 'D' and resid 135 through 139 removed outlier: 3.906A pdb=" N GLU D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 135 through 139' Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 471 through 475 Processing helix chain 'D' and resid 519 through 527 Processing helix chain 'D' and resid 544 through 551 removed outlier: 3.630A pdb=" N ILE D 548 " --> pdb=" O GLY D 544 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 573 removed outlier: 4.300A pdb=" N GLU D 573 " --> pdb=" O GLN D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 600 Processing helix chain 'D' and resid 615 through 622 removed outlier: 4.277A pdb=" N GLY D 621 " --> pdb=" O ALA D 617 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER D 622 " --> pdb=" O SER D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 634 removed outlier: 3.838A pdb=" N MET D 630 " --> pdb=" O PRO D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 655 Processing helix chain 'D' and resid 656 through 663 Proline residue: D 661 - end of helix Processing helix chain 'D' and resid 680 through 693 removed outlier: 3.570A pdb=" N ARG D 693 " --> pdb=" O VAL D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 730 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 31 removed outlier: 5.534A pdb=" N LEU A 26 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR A 51 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 28 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG A 42 " --> pdb=" O HIS A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 removed outlier: 4.146A pdb=" N ARG A 42 " --> pdb=" O HIS A 71 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG A 62 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 96 removed outlier: 5.718A pdb=" N GLU A 91 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS A 108 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 131 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU A 125 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LYS A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 251 removed outlier: 6.584A pdb=" N TRP A 263 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLN A 248 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL A 261 " --> pdb=" O GLN A 248 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 307 removed outlier: 3.612A pdb=" N ALA A 301 " --> pdb=" O PHE A 319 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 315 " --> pdb=" O PRO A 305 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU A 307 " --> pdb=" O ARG A 313 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ARG A 313 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 331 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 340 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 375 through 382 removed outlier: 3.571A pdb=" N SER A 380 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP A 387 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 409 through 416 removed outlier: 5.521A pdb=" N TRP A 410 " --> pdb=" O SER A 425 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N SER A 425 " --> pdb=" O TRP A 410 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU A 412 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLN A 423 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 414 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A 433 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 461 through 468 removed outlier: 3.729A pdb=" N GLU A 485 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL A 503 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL A 535 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N MET A 505 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 606 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET A 670 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 25 through 31 removed outlier: 5.516A pdb=" N LEU B 26 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR B 51 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 28 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG B 42 " --> pdb=" O HIS B 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 35 through 36 removed outlier: 4.477A pdb=" N ARG B 42 " --> pdb=" O HIS B 71 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG B 62 " --> pdb=" O THR B 88 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 91 through 96 removed outlier: 5.947A pdb=" N GLU B 91 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS B 108 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 93 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLN B 119 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASN B 134 " --> pdb=" O GLN B 119 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 121 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER B 132 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL B 123 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AB6, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AB7, first strand: chain 'B' and resid 244 through 251 removed outlier: 6.457A pdb=" N TRP B 263 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLN B 248 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL B 261 " --> pdb=" O GLN B 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 301 through 307 removed outlier: 3.595A pdb=" N ALA B 301 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B 315 " --> pdb=" O PRO B 305 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU B 307 " --> pdb=" O ARG B 313 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ARG B 313 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL B 340 " --> pdb=" O ASP B 335 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 375 through 381 removed outlier: 3.615A pdb=" N SER B 380 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP B 387 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 409 through 416 removed outlier: 5.581A pdb=" N TRP B 410 " --> pdb=" O SER B 425 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N SER B 425 " --> pdb=" O TRP B 410 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU B 412 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLN B 423 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B 433 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 461 through 468 removed outlier: 3.719A pdb=" N GLU B 485 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 10.240A pdb=" N VAL B 500 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG B 580 " --> pdb=" O VAL B 500 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET B 502 " --> pdb=" O ARG B 580 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 585 through 586 Processing sheet with id=AC4, first strand: chain 'C' and resid 25 through 31 removed outlier: 6.600A pdb=" N GLU C 49 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA C 29 " --> pdb=" O HIS C 47 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS C 47 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU C 31 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N THR C 45 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG C 42 " --> pdb=" O HIS C 71 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 35 through 36 removed outlier: 4.274A pdb=" N ARG C 42 " --> pdb=" O HIS C 71 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG C 62 " --> pdb=" O THR C 88 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 91 through 96 removed outlier: 5.959A pdb=" N GLU C 91 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS C 108 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 93 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS C 131 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLU C 125 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LYS C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AC8, first strand: chain 'C' and resid 173 through 174 Processing sheet with id=AC9, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AD1, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AD2, first strand: chain 'C' and resid 301 through 307 removed outlier: 3.564A pdb=" N ALA C 301 " --> pdb=" O PHE C 319 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL C 315 " --> pdb=" O PRO C 305 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU C 307 " --> pdb=" O ARG C 313 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG C 313 " --> pdb=" O LEU C 307 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 375 through 382 removed outlier: 3.567A pdb=" N SER C 380 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP C 387 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 409 through 416 removed outlier: 5.632A pdb=" N TRP C 410 " --> pdb=" O SER C 425 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N SER C 425 " --> pdb=" O TRP C 410 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU C 412 " --> pdb=" O GLN C 423 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLN C 423 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C 414 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU C 433 " --> pdb=" O LEU C 452 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 461 through 468 removed outlier: 3.589A pdb=" N GLU C 485 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 535 " --> pdb=" O MET C 505 " (cutoff:3.500A) removed outlier: 10.301A pdb=" N VAL C 500 " --> pdb=" O ALA C 578 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG C 580 " --> pdb=" O VAL C 500 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA C 606 " --> pdb=" O VAL C 581 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 25 through 31 removed outlier: 6.735A pdb=" N GLU D 49 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA D 29 " --> pdb=" O HIS D 47 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N HIS D 47 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU D 31 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR D 45 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG D 42 " --> pdb=" O HIS D 71 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 35 through 36 removed outlier: 4.242A pdb=" N ARG D 42 " --> pdb=" O HIS D 71 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG D 62 " --> pdb=" O THR D 88 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 91 through 96 removed outlier: 6.836A pdb=" N LEU D 106 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER D 94 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALA D 104 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLU D 96 " --> pdb=" O MET D 102 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N MET D 102 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU D 125 " --> pdb=" O LYS D 129 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LYS D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 153 through 155 Processing sheet with id=AE1, first strand: chain 'D' and resid 173 through 174 Processing sheet with id=AE2, first strand: chain 'D' and resid 244 through 251 removed outlier: 6.573A pdb=" N TRP D 263 " --> pdb=" O PRO D 246 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLN D 248 " --> pdb=" O VAL D 261 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL D 261 " --> pdb=" O GLN D 248 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 301 through 307 removed outlier: 3.592A pdb=" N ALA D 301 " --> pdb=" O PHE D 319 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL D 315 " --> pdb=" O PRO D 305 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU D 307 " --> pdb=" O ARG D 313 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ARG D 313 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU D 331 " --> pdb=" O VAL D 344 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 375 through 382 Processing sheet with id=AE5, first strand: chain 'D' and resid 409 through 416 removed outlier: 5.470A pdb=" N TRP D 410 " --> pdb=" O SER D 425 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N SER D 425 " --> pdb=" O TRP D 410 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU D 412 " --> pdb=" O GLN D 423 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLN D 423 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU D 433 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 461 through 468 removed outlier: 3.870A pdb=" N GLU D 485 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 535 " --> pdb=" O MET D 505 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET D 502 " --> pdb=" O ALA D 582 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N AMET D 584 " --> pdb=" O MET D 502 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL D 504 " --> pdb=" O AMET D 584 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N AGLY D 586 " --> pdb=" O VAL D 504 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 610 " --> pdb=" O BGLY D 585 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N BSER D 587 " --> pdb=" O ARG D 610 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLY D 672 " --> pdb=" O ASN D 611 " (cutoff:3.500A) 847 hydrogen bonds defined for protein. 2382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.19 Time building geometry restraints manager: 7.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6923 1.34 - 1.46: 4673 1.46 - 1.58: 10187 1.58 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 21999 Sorted by residual: bond pdb=" CG PRO B 552 " pdb=" CD PRO B 552 " ideal model delta sigma weight residual 1.503 1.547 -0.044 3.40e-02 8.65e+02 1.69e+00 bond pdb=" CB PRO D 459 " pdb=" CG PRO D 459 " ideal model delta sigma weight residual 1.492 1.549 -0.057 5.00e-02 4.00e+02 1.28e+00 bond pdb=" CB PRO C 459 " pdb=" CG PRO C 459 " ideal model delta sigma weight residual 1.492 1.548 -0.056 5.00e-02 4.00e+02 1.28e+00 bond pdb=" CB PRO B 552 " pdb=" CG PRO B 552 " ideal model delta sigma weight residual 1.492 1.544 -0.052 5.00e-02 4.00e+02 1.10e+00 bond pdb=" C ILE A 272 " pdb=" O ILE A 272 " ideal model delta sigma weight residual 1.236 1.225 0.012 1.19e-02 7.06e+03 9.51e-01 ... (remaining 21994 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.57: 907 106.57 - 113.43: 11771 113.43 - 120.29: 7482 120.29 - 127.15: 9494 127.15 - 134.01: 338 Bond angle restraints: 29992 Sorted by residual: angle pdb=" C LYS D 126 " pdb=" CA LYS D 126 " pdb=" CB LYS D 126 " ideal model delta sigma weight residual 117.23 110.33 6.90 1.36e+00 5.41e-01 2.58e+01 angle pdb=" CA PRO B 552 " pdb=" N PRO B 552 " pdb=" CD PRO B 552 " ideal model delta sigma weight residual 112.00 106.68 5.32 1.40e+00 5.10e-01 1.44e+01 angle pdb=" CA LYS D 126 " pdb=" C LYS D 126 " pdb=" N ASN D 127 " ideal model delta sigma weight residual 119.98 116.88 3.10 8.50e-01 1.38e+00 1.33e+01 angle pdb=" N BGLY A 586 " pdb=" CA BGLY A 586 " pdb=" C BGLY A 586 " ideal model delta sigma weight residual 113.18 120.66 -7.48 2.37e+00 1.78e-01 9.96e+00 angle pdb=" C AGLY C 586 " pdb=" N ASER C 587 " pdb=" CA ASER C 587 " ideal model delta sigma weight residual 121.54 127.04 -5.50 1.91e+00 2.74e-01 8.30e+00 ... (remaining 29987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 12043 17.73 - 35.46: 763 35.46 - 53.18: 102 53.18 - 70.91: 40 70.91 - 88.64: 16 Dihedral angle restraints: 12964 sinusoidal: 4835 harmonic: 8129 Sorted by residual: dihedral pdb=" CA ASER C 587 " pdb=" C ASER C 587 " pdb=" N AHIS C 588 " pdb=" CA AHIS C 588 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CB GLU A 454 " pdb=" CG GLU A 454 " pdb=" CD GLU A 454 " pdb=" OE1 GLU A 454 " ideal model delta sinusoidal sigma weight residual 0.00 88.64 -88.64 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU B 454 " pdb=" CG GLU B 454 " pdb=" CD GLU B 454 " pdb=" OE1 GLU B 454 " ideal model delta sinusoidal sigma weight residual 0.00 -88.63 88.63 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 12961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1869 0.027 - 0.054: 864 0.054 - 0.081: 301 0.081 - 0.107: 186 0.107 - 0.134: 110 Chirality restraints: 3330 Sorted by residual: chirality pdb=" CA VAL B 240 " pdb=" N VAL B 240 " pdb=" C VAL B 240 " pdb=" CB VAL B 240 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE A 314 " pdb=" N ILE A 314 " pdb=" C ILE A 314 " pdb=" CB ILE A 314 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE B 314 " pdb=" N ILE B 314 " pdb=" C ILE B 314 " pdb=" CB ILE B 314 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 3327 not shown) Planarity restraints: 3861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 551 " 0.072 5.00e-02 4.00e+02 1.06e-01 1.80e+01 pdb=" N PRO B 552 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO B 552 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 552 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 551 " -0.059 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO D 552 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO D 552 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 552 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 551 " 0.048 5.00e-02 4.00e+02 7.19e-02 8.26e+00 pdb=" N PRO A 552 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 552 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 552 " 0.040 5.00e-02 4.00e+02 ... (remaining 3858 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3159 2.77 - 3.30: 17917 3.30 - 3.83: 32600 3.83 - 4.37: 38986 4.37 - 4.90: 72960 Nonbonded interactions: 165622 Sorted by model distance: nonbonded pdb=" OG SER C 308 " pdb=" OD1 ASP C 310 " model vdw 2.236 2.440 nonbonded pdb=" OG SER D 308 " pdb=" OD1 ASP D 310 " model vdw 2.236 2.440 nonbonded pdb=" OG SER B 308 " pdb=" OD1 ASP B 310 " model vdw 2.284 2.440 nonbonded pdb=" OG SER A 308 " pdb=" OD1 ASP A 310 " model vdw 2.317 2.440 nonbonded pdb=" O SER B 304 " pdb=" OG SER B 304 " model vdw 2.318 2.440 ... (remaining 165617 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 9 through 38 or resid 40 through 127 or resid 129 through \ 156 or resid 158 through 179 or (resid 180 through 200 and (name N or name CA or \ name C or name O or name CB )) or resid 201 through 217 or (resid 218 and (name \ N or name CA or name C or name O or name CB )) or resid 219 through 287 or (res \ id 288 and (name N or name CA or name C or name O or name CB )) or resid 289 thr \ ough 350 or (resid 351 and (name N or name CA or name C or name O or name CB )) \ or resid 352 through 396 or (resid 397 and (name N or name CA or name C or name \ O or name CB )) or resid 398 through 492 or (resid 493 and (name N or name CA or \ name C or name O or name CB )) or resid 494 through 583 or resid 592 through 63 \ 7 or (resid 638 and (name N or name CA or name C or name O or name CB )) or resi \ d 639 through 731 or (resid 732 and (name N or name CA or name C or name O or na \ me CB )))) selection = (chain 'B' and (resid 9 through 38 or resid 40 through 48 or (resid 49 and (name \ N or name CA or name C or name O or name CB )) or resid 50 through 116 or (resi \ d 117 and (name N or name CA or name C or name O or name CB )) or resid 118 thro \ ugh 127 or resid 129 through 156 or resid 158 through 173 or (resid 174 and (nam \ e N or name CA or name C or name O or name CB )) or resid 175 through 217 or (re \ sid 218 and (name N or name CA or name C or name O or name CB )) or resid 219 th \ rough 287 or (resid 288 and (name N or name CA or name C or name O or name CB )) \ or resid 289 through 290 or (resid 291 and (name N or name CA or name C or name \ O or name CB or name CG )) or resid 292 through 492 or (resid 493 and (name N o \ r name CA or name C or name O or name CB )) or resid 494 through 574 or (resid 5 \ 75 and (name N or name CA or name C or name O or name CB )) or resid 576 through \ 583 or resid 592 through 637 or (resid 638 and (name N or name CA or name C or \ name O or name CB )) or resid 639 through 641 or (resid 642 and (name N or name \ CA or name C or name O or name CB )) or resid 643 through 693 or (resid 694 and \ (name N or name CA or name C or name O or name CB )) or resid 695 through 732)) selection = (chain 'C' and (resid 9 through 48 or (resid 49 and (name N or name CA or name C \ or name O or name CB )) or resid 50 through 116 or (resid 117 and (name N or na \ me CA or name C or name O or name CB )) or resid 118 through 127 or resid 129 th \ rough 156 or resid 158 through 173 or (resid 174 and (name N or name CA or name \ C or name O or name CB )) or resid 175 through 179 or (resid 180 through 200 and \ (name N or name CA or name C or name O or name CB )) or resid 201 through 290 o \ r (resid 291 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 292 through 396 or (resid 397 and (name N or name CA or name C or name \ O or name CB )) or resid 398 through 492 or (resid 493 and (name N or name CA o \ r name C or name O or name CB )) or resid 494 through 574 or (resid 575 and (nam \ e N or name CA or name C or name O or name CB )) or resid 576 through 583 or res \ id 592 through 637 or (resid 638 and (name N or name CA or name C or name O or n \ ame CB )) or resid 639 through 641 or (resid 642 and (name N or name CA or name \ C or name O or name CB )) or resid 643 through 693 or (resid 694 and (name N or \ name CA or name C or name O or name CB )) or resid 695 through 731 or (resid 732 \ and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 9 through 48 or (resid 49 and (name N or name CA or name C \ or name O or name CB )) or resid 50 through 127 or resid 129 through 156 or res \ id 158 through 173 or (resid 174 and (name N or name CA or name C or name O or n \ ame CB )) or resid 175 through 179 or (resid 180 through 200 and (name N or name \ CA or name C or name O or name CB )) or resid 201 through 217 or (resid 218 and \ (name N or name CA or name C or name O or name CB )) or resid 219 through 287 o \ r (resid 288 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 89 through 290 or (resid 291 and (name N or name CA or name C or name O or name \ CB or name CG )) or resid 292 through 350 or (resid 351 and (name N or name CA o \ r name C or name O or name CB )) or resid 352 through 396 or (resid 397 and (nam \ e N or name CA or name C or name O or name CB )) or resid 398 through 415 or (re \ sid 416 and (name N or name CA or name C or name O or name CB )) or resid 417 th \ rough 572 or (resid 573 through 575 and (name N or name CA or name C or name O o \ r name CB )) or resid 576 through 583 or resid 592 through 641 or (resid 642 and \ (name N or name CA or name C or name O or name CB )) or resid 643 through 693 o \ r (resid 694 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 95 through 731 or (resid 732 and (name N or name CA or name C or name O or name \ CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 1.610 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: 7.640 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 70.640 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 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 : 0.002 0.057 21999 Z= 0.162 Angle : 0.521 7.479 29992 Z= 0.280 Chirality : 0.043 0.134 3330 Planarity : 0.005 0.106 3861 Dihedral : 12.521 88.637 7748 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.05 % Allowed : 0.32 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.37 (0.15), residues: 2808 helix: 0.66 (0.24), residues: 481 sheet: 0.90 (0.17), residues: 892 loop : -1.37 (0.14), residues: 1435 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.589 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.3118 time to fit residues: 98.4940 Evaluate side-chains 162 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.300 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 132 optimal weight: 0.5980 chunk 162 optimal weight: 0.0670 chunk 252 optimal weight: 7.9990 overall best weight: 1.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 673 GLN B 673 GLN C 673 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21999 Z= 0.285 Angle : 0.591 10.443 29992 Z= 0.303 Chirality : 0.047 0.139 3330 Planarity : 0.005 0.079 3861 Dihedral : 4.067 26.392 3056 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.41 % Allowed : 4.21 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.30 (0.15), residues: 2808 helix: 1.03 (0.23), residues: 493 sheet: 0.88 (0.17), residues: 896 loop : -1.43 (0.14), residues: 1419 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 162 time to evaluate : 2.544 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 167 average time/residue: 0.3448 time to fit residues: 90.2148 Evaluate side-chains 163 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 156 time to evaluate : 2.389 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2016 time to fit residues: 5.7772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 210 optimal weight: 0.9980 chunk 171 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 252 optimal weight: 4.9990 chunk 273 optimal weight: 6.9990 chunk 225 optimal weight: 8.9990 chunk 250 optimal weight: 5.9990 chunk 86 optimal weight: 0.0370 chunk 202 optimal weight: 0.0060 overall best weight: 0.5074 ------------------------------------------------------------------------------- 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: 0.8310 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21999 Z= 0.127 Angle : 0.488 8.495 29992 Z= 0.251 Chirality : 0.043 0.130 3330 Planarity : 0.005 0.070 3861 Dihedral : 3.774 27.457 3056 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.23 % Allowed : 4.93 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.08 (0.15), residues: 2808 helix: 1.32 (0.24), residues: 499 sheet: 0.98 (0.17), residues: 896 loop : -1.31 (0.15), residues: 1413 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 174 time to evaluate : 2.214 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 174 average time/residue: 0.3670 time to fit residues: 98.9215 Evaluate side-chains 160 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 2.253 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2024 time to fit residues: 3.4151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 0.8980 chunk 190 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 253 optimal weight: 0.9990 chunk 268 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 240 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN B 66 GLN B 673 GLN C 673 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21999 Z= 0.285 Angle : 0.569 11.869 29992 Z= 0.292 Chirality : 0.046 0.138 3330 Planarity : 0.005 0.067 3861 Dihedral : 4.024 28.651 3056 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.45 % Allowed : 6.15 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.17 (0.15), residues: 2808 helix: 1.26 (0.24), residues: 499 sheet: 0.92 (0.17), residues: 900 loop : -1.38 (0.14), residues: 1409 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 155 time to evaluate : 2.398 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 160 average time/residue: 0.3361 time to fit residues: 85.8531 Evaluate side-chains 155 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 2.572 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1880 time to fit residues: 5.1225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 0.6980 chunk 152 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 200 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 229 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN B 673 GLN C 595 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21999 Z= 0.334 Angle : 0.596 13.093 29992 Z= 0.307 Chirality : 0.048 0.138 3330 Planarity : 0.005 0.065 3861 Dihedral : 4.203 28.709 3056 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.59 % Allowed : 6.56 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.33 (0.15), residues: 2808 helix: 1.18 (0.23), residues: 495 sheet: 0.73 (0.17), residues: 918 loop : -1.45 (0.14), residues: 1395 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 155 time to evaluate : 2.416 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 162 average time/residue: 0.3415 time to fit residues: 87.9434 Evaluate side-chains 158 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 152 time to evaluate : 2.385 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1982 time to fit residues: 5.4118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 0.7980 chunk 241 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 268 optimal weight: 2.9990 chunk 223 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN B 673 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21999 Z= 0.172 Angle : 0.506 10.165 29992 Z= 0.261 Chirality : 0.043 0.130 3330 Planarity : 0.005 0.063 3861 Dihedral : 3.909 28.039 3056 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.45 % Allowed : 7.06 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.15 (0.15), residues: 2808 helix: 1.38 (0.24), residues: 495 sheet: 0.92 (0.17), residues: 896 loop : -1.39 (0.15), residues: 1417 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 160 time to evaluate : 2.690 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 166 average time/residue: 0.3714 time to fit residues: 97.3518 Evaluate side-chains 155 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 2.367 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2059 time to fit residues: 3.8788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 259 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 153 optimal weight: 0.0980 chunk 196 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 267 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- 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: 0.8399 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 21999 Z= 0.427 Angle : 0.643 14.346 29992 Z= 0.331 Chirality : 0.050 0.147 3330 Planarity : 0.006 0.061 3861 Dihedral : 4.349 29.311 3056 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.59 % Allowed : 7.56 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.43 (0.15), residues: 2808 helix: 1.08 (0.23), residues: 495 sheet: 0.69 (0.17), residues: 912 loop : -1.52 (0.14), residues: 1401 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 2.460 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 150 average time/residue: 0.3420 time to fit residues: 82.7959 Evaluate side-chains 148 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 2.312 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2208 time to fit residues: 4.8475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 165 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 52 optimal weight: 0.0050 chunk 51 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 210 optimal weight: 0.6980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 325 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21999 Z= 0.145 Angle : 0.504 10.404 29992 Z= 0.261 Chirality : 0.043 0.142 3330 Planarity : 0.005 0.061 3861 Dihedral : 3.960 27.679 3056 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.27 % Allowed : 7.87 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.15), residues: 2808 helix: 1.31 (0.23), residues: 497 sheet: 0.84 (0.17), residues: 906 loop : -1.41 (0.15), residues: 1405 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 159 time to evaluate : 2.701 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 161 average time/residue: 0.3709 time to fit residues: 93.9657 Evaluate side-chains 154 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 2.555 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2006 time to fit residues: 3.8495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 243 optimal weight: 3.9990 chunk 256 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 249 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 chunk 76 optimal weight: 0.5980 chunk 225 optimal weight: 9.9990 chunk 236 optimal weight: 0.6980 chunk 248 optimal weight: 0.0670 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 673 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21999 Z= 0.194 Angle : 0.514 10.903 29992 Z= 0.265 Chirality : 0.044 0.144 3330 Planarity : 0.005 0.061 3861 Dihedral : 3.898 28.411 3056 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.32 % Allowed : 8.01 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 2808 helix: 1.35 (0.24), residues: 501 sheet: 0.88 (0.17), residues: 904 loop : -1.35 (0.15), residues: 1403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 151 time to evaluate : 2.536 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 152 average time/residue: 0.3642 time to fit residues: 88.4701 Evaluate side-chains 154 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 151 time to evaluate : 2.641 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2215 time to fit residues: 4.7306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 163 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 276 optimal weight: 0.6980 chunk 254 optimal weight: 4.9990 chunk 220 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 170 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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: 0.8351 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21999 Z= 0.208 Angle : 0.519 11.140 29992 Z= 0.268 Chirality : 0.044 0.145 3330 Planarity : 0.005 0.061 3861 Dihedral : 3.900 28.221 3056 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.18 % Allowed : 8.05 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 2808 helix: 1.38 (0.23), residues: 503 sheet: 0.89 (0.17), residues: 904 loop : -1.36 (0.15), residues: 1401 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 2.480 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.3413 time to fit residues: 83.7473 Evaluate side-chains 151 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 3.778 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 175 optimal weight: 0.2980 chunk 234 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 203 optimal weight: 0.0970 chunk 32 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 220 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.110907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.087836 restraints weight = 123443.236| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 5.95 r_work: 0.2457 rms_B_bonded: 5.47 restraints_weight: 2.0000 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2451 r_free = 0.2451 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2450 r_free = 0.2450 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21999 Z= 0.128 Angle : 0.467 9.012 29992 Z= 0.241 Chirality : 0.043 0.139 3330 Planarity : 0.005 0.062 3861 Dihedral : 3.641 27.798 3056 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.23 % Allowed : 8.10 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.04 (0.15), residues: 2808 helix: 1.59 (0.24), residues: 503 sheet: 1.01 (0.17), residues: 896 loop : -1.27 (0.15), residues: 1409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3780.52 seconds wall clock time: 69 minutes 47.23 seconds (4187.23 seconds total)