Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 19:08:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5v_31468/04_2023/7f5v_31468.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5v_31468/04_2023/7f5v_31468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5v_31468/04_2023/7f5v_31468.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5v_31468/04_2023/7f5v_31468.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5v_31468/04_2023/7f5v_31468.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5v_31468/04_2023/7f5v_31468.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 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 120 5.16 5 C 13116 2.51 5 N 3688 2.21 5 O 3988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 49": "OE1" <-> "OE2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A ASP 158": "OD1" <-> "OD2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A ASP 266": "OD1" <-> "OD2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A ARG 411": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A GLU 608": "OE1" <-> "OE2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 683": "OD1" <-> "OD2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B ASP 256": "OD1" <-> "OD2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B ASP 266": "OD1" <-> "OD2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ASP 379": "OD1" <-> "OD2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B ASP 390": "OD1" <-> "OD2" Residue "B ARG 411": "NH1" <-> "NH2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B ARG 551": "NH1" <-> "NH2" Residue "B ARG 576": "NH1" <-> "NH2" Residue "B GLU 608": "OE1" <-> "OE2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 683": "OD1" <-> "OD2" Residue "B ARG 694": "NH1" <-> "NH2" Residue "B ARG 766": "NH1" <-> "NH2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C ASP 158": "OD1" <-> "OD2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C ASP 247": "OD1" <-> "OD2" Residue "C ASP 256": "OD1" <-> "OD2" Residue "C GLU 265": "OE1" <-> "OE2" Residue "C ASP 266": "OD1" <-> "OD2" Residue "C TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C ARG 330": "NH1" <-> "NH2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ASP 379": "OD1" <-> "OD2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ASP 390": "OD1" <-> "OD2" Residue "C ARG 411": "NH1" <-> "NH2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C ARG 551": "NH1" <-> "NH2" Residue "C ARG 576": "NH1" <-> "NH2" Residue "C GLU 608": "OE1" <-> "OE2" Residue "C ARG 625": "NH1" <-> "NH2" Residue "C TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 683": "OD1" <-> "OD2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "C ARG 766": "NH1" <-> "NH2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D ASP 158": "OD1" <-> "OD2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "D ASP 247": "OD1" <-> "OD2" Residue "D ASP 256": "OD1" <-> "OD2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D ASP 266": "OD1" <-> "OD2" Residue "D TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 308": "NH1" <-> "NH2" Residue "D GLU 320": "OE1" <-> "OE2" Residue "D ARG 330": "NH1" <-> "NH2" Residue "D PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 341": "OE1" <-> "OE2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D ASP 379": "OD1" <-> "OD2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ASP 390": "OD1" <-> "OD2" Residue "D ARG 411": "NH1" <-> "NH2" Residue "D ARG 439": "NH1" <-> "NH2" Residue "D ARG 469": "NH1" <-> "NH2" Residue "D ARG 551": "NH1" <-> "NH2" Residue "D ARG 576": "NH1" <-> "NH2" Residue "D GLU 608": "OE1" <-> "OE2" Residue "D ARG 625": "NH1" <-> "NH2" Residue "D TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 683": "OD1" <-> "OD2" Residue "D ARG 694": "NH1" <-> "NH2" Residue "D ARG 766": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 20912 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5228 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 665} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 5228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5228 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 665} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 5228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5228 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 665} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 5228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5228 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 665} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 10.35, per 1000 atoms: 0.49 Number of scatterers: 20912 At special positions: 0 Unit cell: (193.98, 98.58, 94.34, 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 120 16.00 O 3988 8.00 N 3688 7.00 C 13116 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: 8.27 Conformation dependent library (CDL) restraints added in 2.9 seconds 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5144 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 20 sheets defined 47.1% alpha, 9.4% 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 51 through 56 removed outlier: 4.140A pdb=" N LYS A 54 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A 55 " --> pdb=" O GLN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 69 removed outlier: 3.698A pdb=" N ILE A 68 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 69' Processing helix chain 'A' and resid 77 through 93 Processing helix chain 'A' and resid 104 through 119 removed outlier: 3.748A pdb=" N PHE A 108 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.767A pdb=" N LEU A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 163 Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 296 through 307 Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 348 through 363 removed outlier: 3.579A pdb=" N ALA A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 384 Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.858A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 Processing helix chain 'A' and resid 415 through 433 removed outlier: 3.572A pdb=" N GLY A 425 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 481 removed outlier: 3.606A pdb=" N ALA A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 513 Processing helix chain 'A' and resid 527 through 534 removed outlier: 3.689A pdb=" N LEU A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 557 Processing helix chain 'A' and resid 579 through 592 removed outlier: 3.526A pdb=" N ALA A 583 " --> pdb=" O ASP A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 removed outlier: 3.515A pdb=" N SER A 612 " --> pdb=" O ASP A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 627 removed outlier: 3.554A pdb=" N ASP A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 638 Processing helix chain 'A' and resid 666 through 678 Processing helix chain 'A' and resid 689 through 700 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 757 through 761 Processing helix chain 'B' and resid 51 through 56 removed outlier: 4.140A pdb=" N LYS B 54 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR B 55 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 69 removed outlier: 3.698A pdb=" N ILE B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 64 through 69' Processing helix chain 'B' and resid 77 through 93 Processing helix chain 'B' and resid 104 through 119 removed outlier: 3.748A pdb=" N PHE B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.767A pdb=" N LEU B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 163 Processing helix chain 'B' and resid 175 through 179 Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 296 through 307 Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 348 through 363 removed outlier: 3.579A pdb=" N ALA B 352 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 384 Processing helix chain 'B' and resid 384 through 401 removed outlier: 3.858A pdb=" N LYS B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 Processing helix chain 'B' and resid 415 through 433 removed outlier: 3.572A pdb=" N GLY B 425 " --> pdb=" O ASN B 421 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 481 removed outlier: 3.606A pdb=" N ALA B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 513 Processing helix chain 'B' and resid 527 through 534 removed outlier: 3.689A pdb=" N LEU B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 557 Processing helix chain 'B' and resid 579 through 592 removed outlier: 3.526A pdb=" N ALA B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 613 removed outlier: 3.515A pdb=" N SER B 612 " --> pdb=" O ASP B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 627 removed outlier: 3.554A pdb=" N ASP B 618 " --> pdb=" O ALA B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 638 Processing helix chain 'B' and resid 666 through 678 Processing helix chain 'B' and resid 689 through 700 Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 757 through 761 Processing helix chain 'C' and resid 51 through 56 removed outlier: 4.140A pdb=" N LYS C 54 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR C 55 " --> pdb=" O GLN C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 69 removed outlier: 3.698A pdb=" N ILE C 68 " --> pdb=" O GLY C 64 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 64 through 69' Processing helix chain 'C' and resid 77 through 93 Processing helix chain 'C' and resid 104 through 119 removed outlier: 3.748A pdb=" N PHE C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.767A pdb=" N LEU C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 163 Processing helix chain 'C' and resid 175 through 179 Processing helix chain 'C' and resid 180 through 196 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 296 through 307 Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 348 through 363 removed outlier: 3.579A pdb=" N ALA C 352 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 384 Processing helix chain 'C' and resid 384 through 401 removed outlier: 3.858A pdb=" N LYS C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 Processing helix chain 'C' and resid 415 through 433 removed outlier: 3.572A pdb=" N GLY C 425 " --> pdb=" O ASN C 421 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU C 431 " --> pdb=" O LYS C 427 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER C 433 " --> pdb=" O ILE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 481 removed outlier: 3.606A pdb=" N ALA C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 479 " --> pdb=" O GLN C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 513 Processing helix chain 'C' and resid 527 through 534 removed outlier: 3.689A pdb=" N LEU C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 557 Processing helix chain 'C' and resid 579 through 592 removed outlier: 3.526A pdb=" N ALA C 583 " --> pdb=" O ASP C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 613 removed outlier: 3.515A pdb=" N SER C 612 " --> pdb=" O ASP C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 627 removed outlier: 3.554A pdb=" N ASP C 618 " --> pdb=" O ALA C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 638 Processing helix chain 'C' and resid 666 through 678 Processing helix chain 'C' and resid 689 through 700 Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 757 through 761 Processing helix chain 'D' and resid 51 through 56 removed outlier: 4.140A pdb=" N LYS D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR D 55 " --> pdb=" O GLN D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 removed outlier: 3.698A pdb=" N ILE D 68 " --> pdb=" O GLY D 64 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 64 through 69' Processing helix chain 'D' and resid 77 through 93 Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.748A pdb=" N PHE D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.767A pdb=" N LEU D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 163 Processing helix chain 'D' and resid 175 through 179 Processing helix chain 'D' and resid 180 through 196 Processing helix chain 'D' and resid 234 through 244 Processing helix chain 'D' and resid 296 through 307 Processing helix chain 'D' and resid 322 through 327 Processing helix chain 'D' and resid 348 through 363 removed outlier: 3.579A pdb=" N ALA D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 384 Processing helix chain 'D' and resid 384 through 401 removed outlier: 3.858A pdb=" N LYS D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 411 Processing helix chain 'D' and resid 415 through 433 removed outlier: 3.572A pdb=" N GLY D 425 " --> pdb=" O ASN D 421 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU D 431 " --> pdb=" O LYS D 427 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER D 433 " --> pdb=" O ILE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 481 removed outlier: 3.606A pdb=" N ALA D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D 479 " --> pdb=" O GLN D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 513 Processing helix chain 'D' and resid 527 through 534 removed outlier: 3.689A pdb=" N LEU D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 557 Processing helix chain 'D' and resid 579 through 592 removed outlier: 3.526A pdb=" N ALA D 583 " --> pdb=" O ASP D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 613 removed outlier: 3.515A pdb=" N SER D 612 " --> pdb=" O ASP D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 627 removed outlier: 3.554A pdb=" N ASP D 618 " --> pdb=" O ALA D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 638 Processing helix chain 'D' and resid 666 through 678 Processing helix chain 'D' and resid 689 through 700 Processing helix chain 'D' and resid 740 through 742 No H-bonds generated for 'chain 'D' and resid 740 through 742' Processing helix chain 'D' and resid 757 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 173 removed outlier: 6.926A pdb=" N MET A 100 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N THR A 205 " --> pdb=" O MET A 100 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N THR A 102 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL A 101 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL A 61 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 60 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N MET A 252 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS A 62 " --> pdb=" O MET A 252 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU A 249 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS A 315 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU A 251 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL A 312 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 744 through 749 removed outlier: 7.388A pdb=" N LEU A 450 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG A 445 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU A 452 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG A 443 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN A 454 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 519 through 521 removed outlier: 6.867A pdb=" N LEU A 487 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 464 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU A 463 " --> pdb=" O ILE A 542 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 605 through 606 removed outlier: 3.574A pdb=" N ILE A 606 " --> pdb=" O GLU A 662 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 727 through 728 removed outlier: 3.633A pdb=" N GLY A 736 " --> pdb=" O SER A 728 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 168 through 173 removed outlier: 6.926A pdb=" N MET B 100 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N THR B 205 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N THR B 102 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL B 101 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 61 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 60 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N MET B 252 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS B 62 " --> pdb=" O MET B 252 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU B 249 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS B 315 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU B 251 " --> pdb=" O CYS B 315 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL B 312 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 744 through 749 removed outlier: 7.388A pdb=" N LEU B 450 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG B 445 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU B 452 " --> pdb=" O ARG B 443 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG B 443 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN B 454 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 519 through 521 removed outlier: 6.867A pdb=" N LEU B 487 " --> pdb=" O SER B 520 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 464 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU B 463 " --> pdb=" O ILE B 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 605 through 606 removed outlier: 3.574A pdb=" N ILE B 606 " --> pdb=" O GLU B 662 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 727 through 728 removed outlier: 3.633A pdb=" N GLY B 736 " --> pdb=" O SER B 728 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 168 through 173 removed outlier: 6.926A pdb=" N MET C 100 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N THR C 205 " --> pdb=" O MET C 100 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N THR C 102 " --> pdb=" O THR C 205 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL C 101 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 61 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL C 60 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N MET C 252 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS C 62 " --> pdb=" O MET C 252 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU C 249 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS C 315 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU C 251 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL C 312 " --> pdb=" O PHE C 336 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 744 through 749 removed outlier: 7.388A pdb=" N LEU C 450 " --> pdb=" O ARG C 445 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG C 445 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU C 452 " --> pdb=" O ARG C 443 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG C 443 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN C 454 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 519 through 521 removed outlier: 6.867A pdb=" N LEU C 487 " --> pdb=" O SER C 520 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 464 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU C 463 " --> pdb=" O ILE C 542 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 605 through 606 removed outlier: 3.574A pdb=" N ILE C 606 " --> pdb=" O GLU C 662 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 727 through 728 removed outlier: 3.633A pdb=" N GLY C 736 " --> pdb=" O SER C 728 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 168 through 173 removed outlier: 6.926A pdb=" N MET D 100 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N THR D 205 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N THR D 102 " --> pdb=" O THR D 205 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL D 101 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL D 61 " --> pdb=" O VAL D 101 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL D 60 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N MET D 252 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS D 62 " --> pdb=" O MET D 252 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU D 249 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS D 315 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU D 251 " --> pdb=" O CYS D 315 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL D 312 " --> pdb=" O PHE D 336 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 744 through 749 removed outlier: 7.388A pdb=" N LEU D 450 " --> pdb=" O ARG D 445 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG D 445 " --> pdb=" O LEU D 450 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU D 452 " --> pdb=" O ARG D 443 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG D 443 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN D 454 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 519 through 521 removed outlier: 6.867A pdb=" N LEU D 487 " --> pdb=" O SER D 520 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL D 464 " --> pdb=" O LEU D 488 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU D 463 " --> pdb=" O ILE D 542 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 605 through 606 removed outlier: 3.574A pdb=" N ILE D 606 " --> pdb=" O GLU D 662 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 727 through 728 removed outlier: 3.633A pdb=" N GLY D 736 " --> pdb=" O SER D 728 " (cutoff:3.500A) 888 hydrogen bonds defined for protein. 2544 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: 6.68 Time building geometry restraints manager: 8.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7136 1.34 - 1.46: 3988 1.46 - 1.58: 9896 1.58 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 21220 Sorted by residual: bond pdb=" C GLY C 165 " pdb=" N VAL C 166 " ideal model delta sigma weight residual 1.335 1.314 0.021 1.41e-02 5.03e+03 2.20e+00 bond pdb=" C GLY A 165 " pdb=" N VAL A 166 " ideal model delta sigma weight residual 1.335 1.314 0.021 1.41e-02 5.03e+03 2.20e+00 bond pdb=" C GLY B 165 " pdb=" N VAL B 166 " ideal model delta sigma weight residual 1.335 1.314 0.021 1.41e-02 5.03e+03 2.20e+00 bond pdb=" C GLY D 165 " pdb=" N VAL D 166 " ideal model delta sigma weight residual 1.335 1.314 0.021 1.41e-02 5.03e+03 2.20e+00 bond pdb=" CG ARG C 544 " pdb=" CD ARG C 544 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.34e+00 ... (remaining 21215 not shown) Histogram of bond angle deviations from ideal: 99.23 - 106.19: 524 106.19 - 113.15: 12124 113.15 - 120.11: 7064 120.11 - 127.07: 8804 127.07 - 134.03: 196 Bond angle restraints: 28712 Sorted by residual: angle pdb=" N VAL A 725 " pdb=" CA VAL A 725 " pdb=" C VAL A 725 " ideal model delta sigma weight residual 113.20 109.96 3.24 9.60e-01 1.09e+00 1.14e+01 angle pdb=" N VAL D 725 " pdb=" CA VAL D 725 " pdb=" C VAL D 725 " ideal model delta sigma weight residual 113.20 109.96 3.24 9.60e-01 1.09e+00 1.14e+01 angle pdb=" N VAL C 725 " pdb=" CA VAL C 725 " pdb=" C VAL C 725 " ideal model delta sigma weight residual 113.20 109.96 3.24 9.60e-01 1.09e+00 1.14e+01 angle pdb=" N VAL B 725 " pdb=" CA VAL B 725 " pdb=" C VAL B 725 " ideal model delta sigma weight residual 113.20 109.96 3.24 9.60e-01 1.09e+00 1.14e+01 angle pdb=" N ALA B 339 " pdb=" CA ALA B 339 " pdb=" C ALA B 339 " ideal model delta sigma weight residual 111.75 115.86 -4.11 1.28e+00 6.10e-01 1.03e+01 ... (remaining 28707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 11392 15.07 - 30.14: 1228 30.14 - 45.20: 296 45.20 - 60.27: 52 60.27 - 75.34: 32 Dihedral angle restraints: 13000 sinusoidal: 5068 harmonic: 7932 Sorted by residual: dihedral pdb=" CA VAL D 348 " pdb=" C VAL D 348 " pdb=" N GLU D 349 " pdb=" CA GLU D 349 " ideal model delta harmonic sigma weight residual -180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA VAL C 348 " pdb=" C VAL C 348 " pdb=" N GLU C 349 " pdb=" CA GLU C 349 " ideal model delta harmonic sigma weight residual 180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA VAL A 348 " pdb=" C VAL A 348 " pdb=" N GLU A 349 " pdb=" CA GLU A 349 " ideal model delta harmonic sigma weight residual 180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 12997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1960 0.031 - 0.062: 944 0.062 - 0.092: 280 0.092 - 0.123: 176 0.123 - 0.154: 28 Chirality restraints: 3388 Sorted by residual: chirality pdb=" CA PRO C 347 " pdb=" N PRO C 347 " pdb=" C PRO C 347 " pdb=" CB PRO C 347 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA PRO A 347 " pdb=" N PRO A 347 " pdb=" C PRO A 347 " pdb=" CB PRO A 347 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA PRO D 347 " pdb=" N PRO D 347 " pdb=" C PRO D 347 " pdb=" CB PRO D 347 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 3385 not shown) Planarity restraints: 3720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 643 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO A 644 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 644 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 644 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 643 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO B 644 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 644 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 644 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 643 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO C 644 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 644 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 644 " 0.028 5.00e-02 4.00e+02 ... (remaining 3717 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 408 2.64 - 3.21: 21410 3.21 - 3.77: 31480 3.77 - 4.34: 43910 4.34 - 4.90: 69802 Nonbonded interactions: 167010 Sorted by model distance: nonbonded pdb=" OG1 THR C 687 " pdb=" OD1 ASN C 689 " model vdw 2.076 2.440 nonbonded pdb=" OG1 THR B 687 " pdb=" OD1 ASN B 689 " model vdw 2.076 2.440 nonbonded pdb=" OG1 THR A 687 " pdb=" OD1 ASN A 689 " model vdw 2.076 2.440 nonbonded pdb=" OG1 THR D 687 " pdb=" OD1 ASN D 689 " model vdw 2.076 2.440 nonbonded pdb=" OG SER C 546 " pdb=" OD1 ASP C 548 " model vdw 2.150 2.440 ... (remaining 167005 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 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 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: 7.400 Check model and map are aligned: 0.280 Set scattering table: 0.150 Process input model: 50.900 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.110 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.005 0.035 21220 Z= 0.322 Angle : 0.687 6.442 28712 Z= 0.413 Chirality : 0.044 0.154 3388 Planarity : 0.005 0.052 3720 Dihedral : 13.935 75.336 7856 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.89 % Favored : 92.96 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.69 (0.13), residues: 2728 helix: -2.60 (0.12), residues: 1108 sheet: -3.38 (0.20), residues: 448 loop : -3.40 (0.16), residues: 1172 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 292 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 296 average time/residue: 0.3314 time to fit residues: 149.6497 Evaluate side-chains 212 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.355 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 111 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 131 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 250 optimal weight: 0.0370 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN A 369 GLN A 375 ASN A 392 ASN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 HIS A 675 HIS B 344 ASN B 369 GLN B 375 ASN B 392 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 HIS B 675 HIS C 344 ASN C 369 GLN C 375 ASN C 392 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 HIS C 675 HIS D 344 ASN D 369 GLN D 375 ASN D 392 ASN ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 HIS D 675 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 21220 Z= 0.191 Angle : 0.601 7.622 28712 Z= 0.313 Chirality : 0.044 0.195 3388 Planarity : 0.005 0.045 3720 Dihedral : 4.422 21.829 2932 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.87 % Favored : 93.99 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.86 (0.15), residues: 2728 helix: -0.69 (0.15), residues: 1172 sheet: -2.57 (0.23), residues: 420 loop : -2.88 (0.17), residues: 1136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 272 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 16 residues processed: 300 average time/residue: 0.3019 time to fit residues: 147.7149 Evaluate side-chains 256 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 240 time to evaluate : 2.347 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1939 time to fit residues: 8.9148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 139 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 251 optimal weight: 0.8980 chunk 271 optimal weight: 4.9990 chunk 223 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 GLN B 344 ASN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN C 344 ASN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 639 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 21220 Z= 0.309 Angle : 0.631 10.785 28712 Z= 0.323 Chirality : 0.044 0.156 3388 Planarity : 0.005 0.049 3720 Dihedral : 4.589 21.180 2932 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.33 % Favored : 92.52 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.28 (0.16), residues: 2728 helix: -0.08 (0.15), residues: 1172 sheet: -2.33 (0.24), residues: 424 loop : -2.72 (0.18), residues: 1132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 224 time to evaluate : 2.470 Fit side-chains outliers start: 36 outliers final: 12 residues processed: 256 average time/residue: 0.2788 time to fit residues: 117.9661 Evaluate side-chains 228 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 216 time to evaluate : 2.518 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1810 time to fit residues: 7.5178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 248 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 251 optimal weight: 8.9990 chunk 266 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 238 optimal weight: 40.0000 chunk 71 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 HIS ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN C 272 HIS ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 565 HIS ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 21220 Z= 0.324 Angle : 0.607 7.214 28712 Z= 0.315 Chirality : 0.044 0.148 3388 Planarity : 0.004 0.048 3720 Dihedral : 4.575 21.912 2932 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.18 % Favored : 92.67 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.07 (0.16), residues: 2728 helix: 0.11 (0.15), residues: 1176 sheet: -2.11 (0.26), residues: 412 loop : -2.70 (0.18), residues: 1140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 232 time to evaluate : 2.274 Fit side-chains outliers start: 64 outliers final: 32 residues processed: 276 average time/residue: 0.2731 time to fit residues: 124.1638 Evaluate side-chains 260 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 228 time to evaluate : 2.276 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1793 time to fit residues: 14.1018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 222 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 198 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 227 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 239 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 HIS ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 GLN ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 21220 Z= 0.273 Angle : 0.593 7.237 28712 Z= 0.305 Chirality : 0.043 0.154 3388 Planarity : 0.004 0.047 3720 Dihedral : 4.416 18.891 2932 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.38 % Favored : 93.48 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.16), residues: 2728 helix: 0.15 (0.15), residues: 1204 sheet: -2.29 (0.26), residues: 384 loop : -2.45 (0.18), residues: 1140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 256 time to evaluate : 2.456 Fit side-chains outliers start: 32 outliers final: 5 residues processed: 272 average time/residue: 0.2910 time to fit residues: 129.7499 Evaluate side-chains 245 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 240 time to evaluate : 2.438 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1935 time to fit residues: 5.1113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 89 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 65 optimal weight: 0.0870 chunk 267 optimal weight: 2.9990 chunk 221 optimal weight: 0.6980 chunk 123 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 88 optimal weight: 0.0020 chunk 140 optimal weight: 5.9990 overall best weight: 0.7168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 21220 Z= 0.169 Angle : 0.578 7.916 28712 Z= 0.293 Chirality : 0.042 0.161 3388 Planarity : 0.004 0.043 3720 Dihedral : 4.031 16.872 2932 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.95 % Favored : 94.90 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.17), residues: 2728 helix: 0.66 (0.16), residues: 1180 sheet: -1.99 (0.24), residues: 436 loop : -2.30 (0.19), residues: 1112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 268 time to evaluate : 2.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 20 residues processed: 284 average time/residue: 0.2745 time to fit residues: 130.4146 Evaluate side-chains 268 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 248 time to evaluate : 2.463 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1946 time to fit residues: 10.6685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 257 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 152 optimal weight: 0.8980 chunk 195 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 266 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 21220 Z= 0.346 Angle : 0.663 10.082 28712 Z= 0.331 Chirality : 0.045 0.165 3388 Planarity : 0.004 0.046 3720 Dihedral : 4.386 18.471 2932 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.16), residues: 2728 helix: 0.32 (0.15), residues: 1208 sheet: -2.08 (0.25), residues: 380 loop : -2.41 (0.18), residues: 1140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 252 time to evaluate : 2.284 Fit side-chains outliers start: 30 outliers final: 14 residues processed: 276 average time/residue: 0.2944 time to fit residues: 132.4510 Evaluate side-chains 250 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 236 time to evaluate : 2.604 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2013 time to fit residues: 8.7588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 164 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 169 optimal weight: 30.0000 chunk 181 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 21220 Z= 0.289 Angle : 0.647 13.457 28712 Z= 0.321 Chirality : 0.044 0.151 3388 Planarity : 0.004 0.045 3720 Dihedral : 4.335 18.489 2932 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.72 % Favored : 94.13 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.16), residues: 2728 helix: 0.37 (0.16), residues: 1212 sheet: -1.92 (0.24), residues: 432 loop : -2.29 (0.19), residues: 1084 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 252 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 264 average time/residue: 0.3111 time to fit residues: 134.5672 Evaluate side-chains 252 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 240 time to evaluate : 2.924 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2173 time to fit residues: 8.5805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 241 optimal weight: 6.9990 chunk 254 optimal weight: 6.9990 chunk 232 optimal weight: 0.4980 chunk 247 optimal weight: 20.0000 chunk 149 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 194 optimal weight: 0.0070 chunk 76 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 234 optimal weight: 0.4980 chunk 162 optimal weight: 0.9980 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 GLN ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 GLN ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 21220 Z= 0.176 Angle : 0.623 14.035 28712 Z= 0.305 Chirality : 0.043 0.156 3388 Planarity : 0.004 0.045 3720 Dihedral : 4.005 21.689 2932 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.84 % Favored : 95.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.17), residues: 2728 helix: 0.53 (0.16), residues: 1212 sheet: -1.78 (0.24), residues: 436 loop : -2.03 (0.19), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 2.395 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.2770 time to fit residues: 126.0071 Evaluate side-chains 254 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 2.347 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 262 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 182 optimal weight: 0.6980 chunk 274 optimal weight: 4.9990 chunk 253 optimal weight: 5.9990 chunk 218 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 169 optimal weight: 20.0000 chunk 134 optimal weight: 6.9990 chunk 173 optimal weight: 8.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 ASN ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 21220 Z= 0.291 Angle : 0.648 11.441 28712 Z= 0.325 Chirality : 0.044 0.156 3388 Planarity : 0.004 0.046 3720 Dihedral : 4.158 18.354 2932 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.17), residues: 2728 helix: 0.46 (0.16), residues: 1208 sheet: -1.76 (0.24), residues: 432 loop : -2.16 (0.19), residues: 1088 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 248 time to evaluate : 2.460 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 248 average time/residue: 0.2932 time to fit residues: 118.3601 Evaluate side-chains 251 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 246 time to evaluate : 2.233 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1906 time to fit residues: 4.9918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 201 optimal weight: 7.9990 chunk 32 optimal weight: 30.0000 chunk 60 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 225 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 40 optimal weight: 0.0060 chunk 192 optimal weight: 7.9990 overall best weight: 2.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.152808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.096803 restraints weight = 38968.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.101171 restraints weight = 19314.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.103973 restraints weight = 12806.519| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 21220 Z= 0.305 Angle : 0.665 12.004 28712 Z= 0.334 Chirality : 0.044 0.141 3388 Planarity : 0.004 0.045 3720 Dihedral : 4.268 19.641 2932 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.17), residues: 2728 helix: 0.44 (0.16), residues: 1212 sheet: -1.80 (0.24), residues: 432 loop : -2.16 (0.19), residues: 1084 =============================================================================== Job complete usr+sys time: 3545.82 seconds wall clock time: 65 minutes 56.91 seconds (3956.91 seconds total)