Starting phenix.real_space_refine on Mon Dec 11 21:29:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui0_26521/12_2023/7ui0_26521_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui0_26521/12_2023/7ui0_26521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui0_26521/12_2023/7ui0_26521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui0_26521/12_2023/7ui0_26521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui0_26521/12_2023/7ui0_26521_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui0_26521/12_2023/7ui0_26521_neut.pdb" } resolution = 3.4 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= 0.001 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 90 5.16 5 C 12123 2.51 5 N 3330 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A ARG 423": "NH1" <-> "NH2" Residue "A ARG 427": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 494": "NH1" <-> "NH2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A ARG 515": "NH1" <-> "NH2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A ARG 562": "NH1" <-> "NH2" Residue "A ARG 588": "NH1" <-> "NH2" Residue "A ARG 592": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 605": "NH1" <-> "NH2" Residue "A ARG 624": "NH1" <-> "NH2" Residue "A ARG 627": "NH1" <-> "NH2" Residue "A ARG 638": "NH1" <-> "NH2" Residue "A ARG 639": "NH1" <-> "NH2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ARG 707": "NH1" <-> "NH2" Residue "A ARG 708": "NH1" <-> "NH2" Residue "A ARG 715": "NH1" <-> "NH2" Residue "B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 131": "NH1" <-> "NH2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B ARG 215": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B ARG 245": "NH1" <-> "NH2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ARG 264": "NH1" <-> "NH2" Residue "B ARG 279": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 318": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B ARG 360": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 406": "NH1" <-> "NH2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B ARG 423": "NH1" <-> "NH2" Residue "B ARG 427": "NH1" <-> "NH2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B ARG 494": "NH1" <-> "NH2" Residue "B ARG 505": "NH1" <-> "NH2" Residue "B ARG 515": "NH1" <-> "NH2" Residue "B ARG 523": "NH1" <-> "NH2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B ARG 558": "NH1" <-> "NH2" Residue "B ARG 562": "NH1" <-> "NH2" Residue "B ARG 588": "NH1" <-> "NH2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B ARG 599": "NH1" <-> "NH2" Residue "B ARG 605": "NH1" <-> "NH2" Residue "B ARG 624": "NH1" <-> "NH2" Residue "B ARG 627": "NH1" <-> "NH2" Residue "B ARG 638": "NH1" <-> "NH2" Residue "B ARG 639": "NH1" <-> "NH2" Residue "B ARG 661": "NH1" <-> "NH2" Residue "B ARG 691": "NH1" <-> "NH2" Residue "B ARG 707": "NH1" <-> "NH2" Residue "B ARG 708": "NH1" <-> "NH2" Residue "B ARG 715": "NH1" <-> "NH2" Residue "C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C ARG 215": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 242": "NH1" <-> "NH2" Residue "C ARG 245": "NH1" <-> "NH2" Residue "C ARG 258": "NH1" <-> "NH2" Residue "C ARG 264": "NH1" <-> "NH2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "C ARG 304": "NH1" <-> "NH2" Residue "C ARG 318": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 342": "NH1" <-> "NH2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "C ARG 377": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C ARG 406": "NH1" <-> "NH2" Residue "C ARG 418": "NH1" <-> "NH2" Residue "C ARG 423": "NH1" <-> "NH2" Residue "C ARG 427": "NH1" <-> "NH2" Residue "C ARG 428": "NH1" <-> "NH2" Residue "C ARG 494": "NH1" <-> "NH2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C ARG 515": "NH1" <-> "NH2" Residue "C ARG 523": "NH1" <-> "NH2" Residue "C ARG 543": "NH1" <-> "NH2" Residue "C ARG 557": "NH1" <-> "NH2" Residue "C ARG 558": "NH1" <-> "NH2" Residue "C ARG 562": "NH1" <-> "NH2" Residue "C ARG 588": "NH1" <-> "NH2" Residue "C ARG 592": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 605": "NH1" <-> "NH2" Residue "C ARG 624": "NH1" <-> "NH2" Residue "C ARG 627": "NH1" <-> "NH2" Residue "C ARG 638": "NH1" <-> "NH2" Residue "C ARG 639": "NH1" <-> "NH2" Residue "C ARG 661": "NH1" <-> "NH2" Residue "C ARG 691": "NH1" <-> "NH2" Residue "C ARG 707": "NH1" <-> "NH2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C ARG 715": "NH1" <-> "NH2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "I ARG 98": "NH1" <-> "NH2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L ARG 108": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 45": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N ARG 61": "NH1" <-> "NH2" Residue "N ARG 108": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 19203 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4660 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 548} Chain breaks: 2 Chain: "B" Number of atoms: 4660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4660 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 548} Chain breaks: 2 Chain: "C" Number of atoms: 4660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4660 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 548} Chain breaks: 2 Chain: "H" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 905 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 905 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 905 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 104} Chain: "M" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 104} Chain: "N" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 104} Time building chain proxies: 10.67, per 1000 atoms: 0.56 Number of scatterers: 19203 At special positions: 0 Unit cell: (137.775, 138.6, 186.45, 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 90 16.00 O 3660 8.00 N 3330 7.00 C 12123 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.05 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.05 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 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: 7.07 Conformation dependent library (CDL) restraints added in 3.7 seconds 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 42 sheets defined 16.3% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 303 through 310 removed outlier: 4.022A pdb=" N GLY A 306 " --> pdb=" O TYR A 303 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS A 308 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 411 through 428 removed outlier: 4.479A pdb=" N LYS A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 543 removed outlier: 4.844A pdb=" N THR A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU A 538 " --> pdb=" O HIS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 removed outlier: 3.937A pdb=" N ILE A 550 " --> pdb=" O ASN A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 660 through 664 Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 701 through 710 Processing helix chain 'A' and resid 711 through 717 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 303 through 310 removed outlier: 4.022A pdb=" N GLY B 306 " --> pdb=" O TYR B 303 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS B 308 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 411 through 428 removed outlier: 4.479A pdb=" N LYS B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 543 removed outlier: 4.843A pdb=" N THR B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU B 538 " --> pdb=" O HIS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 removed outlier: 3.938A pdb=" N ILE B 550 " --> pdb=" O ASN B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 660 through 664 Processing helix chain 'B' and resid 690 through 697 Processing helix chain 'B' and resid 701 through 710 Processing helix chain 'B' and resid 711 through 717 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 303 through 310 removed outlier: 4.022A pdb=" N GLY C 306 " --> pdb=" O TYR C 303 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS C 308 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 411 through 428 removed outlier: 4.479A pdb=" N LYS C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 543 removed outlier: 4.844A pdb=" N THR C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU C 538 " --> pdb=" O HIS C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 removed outlier: 3.937A pdb=" N ILE C 550 " --> pdb=" O ASN C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 660 through 664 Processing helix chain 'C' and resid 690 through 697 Processing helix chain 'C' and resid 701 through 710 Processing helix chain 'C' and resid 711 through 717 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 574 through 576 removed outlier: 7.042A pdb=" N TYR A 114 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 127 Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 152 removed outlier: 6.212A pdb=" N LYS A 151 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LYS A 368 " --> pdb=" O LYS A 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 366 through 372 current: chain 'A' and resid 449 through 457 Processing sheet with id=AA4, first strand: chain 'A' and resid 157 through 175 removed outlier: 8.577A pdb=" N TYR A 164 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LYS A 166 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG A 189 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL A 168 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU A 187 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL A 170 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE A 185 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLN A 172 " --> pdb=" O MET A 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 180 through 191 current: chain 'A' and resid 246 through 248 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 246 through 248 current: chain 'A' and resid 287 through 289 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 294 through 295 current: chain 'A' and resid 340 through 345 Processing sheet with id=AA5, first strand: chain 'A' and resid 206 through 207 Processing sheet with id=AA6, first strand: chain 'A' and resid 210 through 215 Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 Processing sheet with id=AA8, first strand: chain 'A' and resid 559 through 563 Processing sheet with id=AA9, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AB1, first strand: chain 'A' and resid 638 through 643 removed outlier: 5.804A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 666 through 667 Processing sheet with id=AB3, first strand: chain 'B' and resid 574 through 576 removed outlier: 7.043A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 145 through 152 removed outlier: 6.212A pdb=" N LYS B 151 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LYS B 368 " --> pdb=" O LYS B 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 366 through 372 current: chain 'B' and resid 449 through 457 Processing sheet with id=AB5, first strand: chain 'B' and resid 157 through 175 removed outlier: 8.578A pdb=" N TYR B 164 " --> pdb=" O PRO B 191 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LYS B 166 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG B 189 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 168 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU B 187 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL B 170 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE B 185 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLN B 172 " --> pdb=" O MET B 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 180 through 191 current: chain 'B' and resid 246 through 248 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 246 through 248 current: chain 'B' and resid 287 through 289 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 294 through 295 current: chain 'B' and resid 340 through 345 Processing sheet with id=AB6, first strand: chain 'B' and resid 206 through 207 Processing sheet with id=AB7, first strand: chain 'B' and resid 210 through 215 Processing sheet with id=AB8, first strand: chain 'B' and resid 376 through 380 Processing sheet with id=AB9, first strand: chain 'B' and resid 559 through 563 Processing sheet with id=AC1, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AC2, first strand: chain 'B' and resid 638 through 643 removed outlier: 5.803A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 666 through 667 Processing sheet with id=AC4, first strand: chain 'C' and resid 574 through 576 removed outlier: 7.042A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 145 through 152 removed outlier: 6.212A pdb=" N LYS C 151 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LYS C 368 " --> pdb=" O LYS C 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 366 through 372 current: chain 'C' and resid 449 through 457 Processing sheet with id=AC6, first strand: chain 'C' and resid 157 through 175 removed outlier: 8.577A pdb=" N TYR C 164 " --> pdb=" O PRO C 191 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LYS C 166 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG C 189 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C 168 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU C 187 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL C 170 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE C 185 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLN C 172 " --> pdb=" O MET C 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 180 through 191 current: chain 'C' and resid 246 through 248 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 246 through 248 current: chain 'C' and resid 287 through 289 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 294 through 295 current: chain 'C' and resid 340 through 345 Processing sheet with id=AC7, first strand: chain 'C' and resid 206 through 207 Processing sheet with id=AC8, first strand: chain 'C' and resid 210 through 215 Processing sheet with id=AC9, first strand: chain 'C' and resid 376 through 380 Processing sheet with id=AD1, first strand: chain 'C' and resid 559 through 563 Processing sheet with id=AD2, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AD3, first strand: chain 'C' and resid 638 through 643 removed outlier: 5.804A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AD5, first strand: chain 'H' and resid 9 through 12 removed outlier: 5.546A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE H 34 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N MET H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AD7, first strand: chain 'I' and resid 9 through 12 removed outlier: 5.546A pdb=" N GLU I 10 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE I 34 " --> pdb=" O MET I 50 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N MET I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 3 through 5 Processing sheet with id=AD9, first strand: chain 'J' and resid 9 through 12 removed outlier: 5.546A pdb=" N GLU J 10 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE J 34 " --> pdb=" O MET J 50 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N MET J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.893A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AE4, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.893A pdb=" N LEU M 33 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.892A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1578 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: 9.04 Time building geometry restraints manager: 7.70 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: 6235 1.34 - 1.46: 4418 1.46 - 1.58: 8895 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 19683 Sorted by residual: bond pdb=" CZ ARG B 624 " pdb=" NH2 ARG B 624 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.59e+00 bond pdb=" CZ ARG A 624 " pdb=" NH2 ARG A 624 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.47e+00 bond pdb=" CZ ARG C 624 " pdb=" NH2 ARG C 624 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.38e+00 bond pdb=" CZ ARG C 588 " pdb=" NH2 ARG C 588 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.13e+00 bond pdb=" CZ ARG A 588 " pdb=" NH2 ARG A 588 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.74e+00 ... (remaining 19678 not shown) Histogram of bond angle deviations from ideal: 99.48 - 106.41: 537 106.41 - 113.35: 10619 113.35 - 120.28: 7130 120.28 - 127.22: 8229 127.22 - 134.15: 233 Bond angle restraints: 26748 Sorted by residual: angle pdb=" CB HIS B 637 " pdb=" CG HIS B 637 " pdb=" CD2 HIS B 637 " ideal model delta sigma weight residual 131.20 125.37 5.83 1.30e+00 5.92e-01 2.01e+01 angle pdb=" CB HIS A 637 " pdb=" CG HIS A 637 " pdb=" CD2 HIS A 637 " ideal model delta sigma weight residual 131.20 125.37 5.83 1.30e+00 5.92e-01 2.01e+01 angle pdb=" CB HIS C 637 " pdb=" CG HIS C 637 " pdb=" CD2 HIS C 637 " ideal model delta sigma weight residual 131.20 125.39 5.81 1.30e+00 5.92e-01 2.00e+01 angle pdb=" CB MET I 81 " pdb=" CG MET I 81 " pdb=" SD MET I 81 " ideal model delta sigma weight residual 112.70 101.22 11.48 3.00e+00 1.11e-01 1.47e+01 angle pdb=" CB MET J 81 " pdb=" CG MET J 81 " pdb=" SD MET J 81 " ideal model delta sigma weight residual 112.70 101.24 11.46 3.00e+00 1.11e-01 1.46e+01 ... (remaining 26743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 10492 17.61 - 35.22: 953 35.22 - 52.83: 159 52.83 - 70.43: 45 70.43 - 88.04: 12 Dihedral angle restraints: 11661 sinusoidal: 4617 harmonic: 7044 Sorted by residual: dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 88 " pdb=" CB CYS N 88 " ideal model delta sinusoidal sigma weight residual -86.00 -144.51 58.51 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual -86.00 -144.47 58.47 1 1.00e+01 1.00e-02 4.58e+01 dihedral pdb=" CB CYS M 23 " pdb=" SG CYS M 23 " pdb=" SG CYS M 88 " pdb=" CB CYS M 88 " ideal model delta sinusoidal sigma weight residual -86.00 -144.45 58.45 1 1.00e+01 1.00e-02 4.58e+01 ... (remaining 11658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2258 0.053 - 0.106: 545 0.106 - 0.159: 83 0.159 - 0.212: 15 0.212 - 0.265: 6 Chirality restraints: 2907 Sorted by residual: chirality pdb=" CA TYR A 653 " pdb=" N TYR A 653 " pdb=" C TYR A 653 " pdb=" CB TYR A 653 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA TYR B 653 " pdb=" N TYR B 653 " pdb=" C TYR B 653 " pdb=" CB TYR B 653 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA TYR C 653 " pdb=" N TYR C 653 " pdb=" C TYR C 653 " pdb=" CB TYR C 653 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 2904 not shown) Planarity restraints: 3456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 653 " -0.066 2.00e-02 2.50e+03 3.43e-02 2.35e+01 pdb=" CG TYR C 653 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR C 653 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR C 653 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR C 653 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR C 653 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 653 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR C 653 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 653 " -0.066 2.00e-02 2.50e+03 3.42e-02 2.34e+01 pdb=" CG TYR A 653 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 653 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A 653 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR A 653 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 653 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 653 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 653 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 653 " -0.065 2.00e-02 2.50e+03 3.42e-02 2.33e+01 pdb=" CG TYR B 653 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 653 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR B 653 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR B 653 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR B 653 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 653 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 653 " -0.041 2.00e-02 2.50e+03 ... (remaining 3453 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 330 2.62 - 3.19: 17473 3.19 - 3.76: 29296 3.76 - 4.33: 40979 4.33 - 4.90: 68164 Nonbonded interactions: 156242 Sorted by model distance: nonbonded pdb=" O GLU A 152 " pdb=" OH TYR B 689 " model vdw 2.052 2.440 nonbonded pdb=" OH TYR B 647 " pdb=" OE1 GLN C 126 " model vdw 2.083 2.440 nonbonded pdb=" OH TYR A 380 " pdb=" OD2 ASP C 680 " model vdw 2.084 2.440 nonbonded pdb=" OD2 ASP A 680 " pdb=" OH TYR B 380 " model vdw 2.097 2.440 nonbonded pdb=" OH TYR C 606 " pdb=" NE2 HIS J 59 " model vdw 2.131 2.520 ... (remaining 156237 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' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 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: 0.020 Extract box with map and model: 13.250 Check model and map are aligned: 0.000 Set scattering table: 0.060 Process input model: 54.620 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.130 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 : 0.008 0.049 19683 Z= 0.502 Angle : 0.812 11.484 26748 Z= 0.486 Chirality : 0.049 0.265 2907 Planarity : 0.006 0.091 3456 Dihedral : 13.944 88.042 7086 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.38 (0.17), residues: 2385 helix: 0.48 (0.29), residues: 309 sheet: -1.10 (0.17), residues: 798 loop : -1.08 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 110 HIS 0.017 0.002 HIS C 637 PHE 0.039 0.003 PHE A 641 TYR 0.066 0.002 TYR C 653 ARG 0.006 0.001 ARG C 627 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.2415 time to fit residues: 115.0750 Evaluate side-chains 232 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 2.176 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A 534 HIS B 216 ASN B 458 ASN B 507 GLN B 534 HIS C 129 GLN C 216 ASN ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN I 82 GLN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN N 79 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19683 Z= 0.220 Angle : 0.582 8.136 26748 Z= 0.307 Chirality : 0.043 0.160 2907 Planarity : 0.004 0.039 3456 Dihedral : 5.027 22.767 2688 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.54 % Allowed : 8.20 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.12 (0.17), residues: 2385 helix: 0.97 (0.30), residues: 315 sheet: -0.91 (0.17), residues: 801 loop : -1.02 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 110 HIS 0.010 0.001 HIS C 534 PHE 0.016 0.002 PHE M 98 TYR 0.025 0.002 TYR B 653 ARG 0.004 0.000 ARG M 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 258 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 18 residues processed: 275 average time/residue: 0.3054 time to fit residues: 130.7000 Evaluate side-chains 235 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 217 time to evaluate : 2.115 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1889 time to fit residues: 9.0198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 232 optimal weight: 30.0000 chunk 192 optimal weight: 30.0000 chunk 213 optimal weight: 30.0000 chunk 73 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 GLN ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 19683 Z= 0.430 Angle : 0.672 13.649 26748 Z= 0.356 Chirality : 0.045 0.176 2907 Planarity : 0.005 0.045 3456 Dihedral : 5.284 23.583 2688 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.03 % Allowed : 11.63 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.38 (0.16), residues: 2385 helix: 0.42 (0.28), residues: 333 sheet: -1.13 (0.17), residues: 747 loop : -1.08 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP I 36 HIS 0.009 0.001 HIS A 516 PHE 0.015 0.002 PHE B 294 TYR 0.037 0.002 TYR A 653 ARG 0.004 0.000 ARG A 627 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 227 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 18 residues processed: 251 average time/residue: 0.2952 time to fit residues: 117.2369 Evaluate side-chains 230 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 212 time to evaluate : 2.364 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1885 time to fit residues: 9.3422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN B 507 GLN ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN N 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 19683 Z= 0.286 Angle : 0.590 9.915 26748 Z= 0.310 Chirality : 0.043 0.164 2907 Planarity : 0.004 0.040 3456 Dihedral : 5.014 22.219 2688 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.78 % Allowed : 13.41 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.17), residues: 2385 helix: 0.96 (0.29), residues: 315 sheet: -1.21 (0.16), residues: 816 loop : -1.03 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 36 HIS 0.006 0.001 HIS A 516 PHE 0.018 0.001 PHE C 294 TYR 0.038 0.001 TYR A 653 ARG 0.003 0.000 ARG C 627 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 231 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 15 residues processed: 253 average time/residue: 0.2992 time to fit residues: 119.6103 Evaluate side-chains 231 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 216 time to evaluate : 2.222 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1888 time to fit residues: 8.3198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 195 optimal weight: 0.8980 chunk 158 optimal weight: 0.0970 chunk 0 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 205 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 ASN L 30 ASN L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19683 Z= 0.259 Angle : 0.592 10.577 26748 Z= 0.310 Chirality : 0.042 0.155 2907 Planarity : 0.004 0.045 3456 Dihedral : 4.914 27.715 2688 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.40 % Allowed : 14.95 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.17), residues: 2385 helix: 1.04 (0.29), residues: 315 sheet: -1.24 (0.16), residues: 849 loop : -0.93 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 36 HIS 0.005 0.001 HIS A 516 PHE 0.023 0.001 PHE C 194 TYR 0.037 0.001 TYR A 653 ARG 0.007 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 229 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 248 average time/residue: 0.2999 time to fit residues: 117.0419 Evaluate side-chains 224 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 211 time to evaluate : 2.127 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1708 time to fit residues: 7.0916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 6.9990 chunk 206 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN N 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19683 Z= 0.346 Angle : 0.615 10.042 26748 Z= 0.323 Chirality : 0.043 0.165 2907 Planarity : 0.004 0.043 3456 Dihedral : 4.980 24.366 2688 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.45 % Allowed : 16.02 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.32 (0.17), residues: 2385 helix: 0.94 (0.29), residues: 315 sheet: -1.35 (0.16), residues: 873 loop : -0.89 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP H 36 HIS 0.007 0.001 HIS A 516 PHE 0.025 0.002 PHE C 194 TYR 0.021 0.002 TYR B 653 ARG 0.007 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 227 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 11 residues processed: 246 average time/residue: 0.3264 time to fit residues: 125.9342 Evaluate side-chains 229 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 218 time to evaluate : 2.081 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1773 time to fit residues: 6.5009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 167 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 228 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 217 ASN ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN N 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19683 Z= 0.229 Angle : 0.580 10.525 26748 Z= 0.305 Chirality : 0.042 0.158 2907 Planarity : 0.004 0.052 3456 Dihedral : 4.815 23.271 2688 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.21 % Allowed : 17.08 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.21 (0.17), residues: 2385 helix: 1.07 (0.29), residues: 315 sheet: -1.25 (0.16), residues: 843 loop : -0.87 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP I 36 HIS 0.004 0.001 HIS A 516 PHE 0.018 0.001 PHE C 194 TYR 0.051 0.001 TYR B 653 ARG 0.007 0.000 ARG B 627 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 232 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 8 residues processed: 249 average time/residue: 0.3093 time to fit residues: 120.8303 Evaluate side-chains 228 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 220 time to evaluate : 2.540 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1867 time to fit residues: 5.8812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 207 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN N 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19683 Z= 0.362 Angle : 0.625 10.368 26748 Z= 0.330 Chirality : 0.044 0.156 2907 Planarity : 0.004 0.049 3456 Dihedral : 4.985 24.165 2688 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.82 % Allowed : 18.23 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.23 (0.17), residues: 2385 helix: 0.95 (0.29), residues: 315 sheet: -1.19 (0.16), residues: 837 loop : -0.91 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP I 36 HIS 0.008 0.001 HIS A 516 PHE 0.019 0.002 PHE A 294 TYR 0.049 0.002 TYR B 653 ARG 0.007 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 224 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 235 average time/residue: 0.3123 time to fit residues: 115.1484 Evaluate side-chains 225 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 219 time to evaluate : 2.157 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1839 time to fit residues: 5.0191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 0.7980 chunk 199 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 chunk 128 optimal weight: 0.0980 chunk 92 optimal weight: 0.2980 chunk 167 optimal weight: 2.9990 chunk 65 optimal weight: 0.0980 chunk 192 optimal weight: 40.0000 chunk 201 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 225 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19683 Z= 0.177 Angle : 0.576 9.262 26748 Z= 0.304 Chirality : 0.042 0.162 2907 Planarity : 0.004 0.039 3456 Dihedral : 4.717 23.229 2688 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.34 % Allowed : 18.81 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.97 (0.17), residues: 2385 helix: 1.14 (0.30), residues: 315 sheet: -0.83 (0.17), residues: 780 loop : -0.92 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP I 36 HIS 0.004 0.001 HIS B 311 PHE 0.022 0.001 PHE C 194 TYR 0.047 0.001 TYR B 653 ARG 0.007 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 226 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 230 average time/residue: 0.3139 time to fit residues: 112.8841 Evaluate side-chains 220 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 216 time to evaluate : 2.205 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1691 time to fit residues: 4.2044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 236 optimal weight: 0.8980 chunk 217 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 149 optimal weight: 0.0000 chunk 200 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 5 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN N 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19683 Z= 0.211 Angle : 0.580 9.327 26748 Z= 0.306 Chirality : 0.042 0.170 2907 Planarity : 0.004 0.059 3456 Dihedral : 4.648 22.076 2688 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.34 % Allowed : 19.01 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.88 (0.17), residues: 2385 helix: 1.18 (0.30), residues: 315 sheet: -0.85 (0.17), residues: 771 loop : -0.79 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP I 36 HIS 0.004 0.001 HIS I 35 PHE 0.022 0.001 PHE C 194 TYR 0.041 0.001 TYR B 653 ARG 0.007 0.000 ARG C 178 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 223 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 226 average time/residue: 0.3016 time to fit residues: 105.9894 Evaluate side-chains 222 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 219 time to evaluate : 2.012 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1733 time to fit residues: 3.6798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 7.9990 chunk 173 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 193 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN L 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.089745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.061034 restraints weight = 51121.001| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.22 r_work: 0.2807 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19683 Z= 0.242 Angle : 0.592 10.950 26748 Z= 0.313 Chirality : 0.043 0.164 2907 Planarity : 0.004 0.043 3456 Dihedral : 4.665 22.128 2688 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.19 % Allowed : 19.10 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.88 (0.17), residues: 2385 helix: 1.22 (0.30), residues: 312 sheet: -0.89 (0.17), residues: 795 loop : -0.77 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP I 36 HIS 0.005 0.001 HIS I 35 PHE 0.024 0.001 PHE C 194 TYR 0.042 0.001 TYR B 653 ARG 0.007 0.000 ARG C 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4045.16 seconds wall clock time: 77 minutes 39.88 seconds (4659.88 seconds total)