Starting phenix.real_space_refine on Sun Mar 17 22:58:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui0_26521/03_2024/7ui0_26521_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui0_26521/03_2024/7ui0_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_26521/03_2024/7ui0_26521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui0_26521/03_2024/7ui0_26521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui0_26521/03_2024/7ui0_26521_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui0_26521/03_2024/7ui0_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-dev-5265/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: 9.82, per 1000 atoms: 0.51 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: 7.87 Conformation dependent library (CDL) restraints added in 3.8 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: 2.45 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: 6.04 Time building geometry restraints manager: 8.52 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: 2.250 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: 10.860 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 52.060 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.600 ------------------------------------------------------------------------------- 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 : 2.289 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 REVERT: B 187 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7736 (mt-10) REVERT: B 419 ASP cc_start: 0.7559 (t70) cc_final: 0.7267 (t0) REVERT: C 297 MET cc_start: 0.8598 (ptm) cc_final: 0.8384 (ptp) REVERT: H 36 TRP cc_start: 0.7374 (m100) cc_final: 0.7052 (m100) REVERT: H 95 TYR cc_start: 0.6671 (m-80) cc_final: 0.6430 (m-80) REVERT: I 10 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6629 (mm-30) REVERT: J 36 TRP cc_start: 0.7687 (m100) cc_final: 0.7235 (m100) REVERT: J 95 TYR cc_start: 0.6871 (m-80) cc_final: 0.6423 (m-80) REVERT: J 112 GLN cc_start: 0.6577 (pm20) cc_final: 0.6182 (pm20) REVERT: L 91 TYR cc_start: 0.8351 (p90) cc_final: 0.8131 (p90) REVERT: M 37 GLN cc_start: 0.7054 (tt0) cc_final: 0.6386 (tm-30) REVERT: M 91 TYR cc_start: 0.8425 (p90) cc_final: 0.8046 (p90) REVERT: N 37 GLN cc_start: 0.6862 (tt0) cc_final: 0.6459 (tt0) REVERT: N 79 GLN cc_start: 0.6698 (pt0) cc_final: 0.6481 (pt0) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.3105 time to fit residues: 146.3488 Evaluate side-chains 237 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 2.365 ------------------------------------------------------------------------------- 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: 4.9990 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 453 GLN ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN I 82 GLN L 79 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19683 Z= 0.217 Angle : 0.586 8.838 26748 Z= 0.308 Chirality : 0.044 0.170 2907 Planarity : 0.004 0.039 3456 Dihedral : 5.018 21.363 2688 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.59 % Allowed : 8.06 % Favored : 90.35 % 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: -1.12 (0.17), residues: 2385 helix: 0.98 (0.30), residues: 315 sheet: -0.89 (0.17), residues: 801 loop : -1.03 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 36 HIS 0.011 0.001 HIS C 534 PHE 0.015 0.002 PHE A 287 TYR 0.027 0.002 TYR B 653 ARG 0.004 0.000 ARG A 624 *********************** 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 298 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 265 time to evaluate : 2.435 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: A 520 MET cc_start: 0.8083 (mmp) cc_final: 0.7861 (mmp) REVERT: B 194 PHE cc_start: 0.7725 (m-80) cc_final: 0.7509 (m-80) REVERT: B 419 ASP cc_start: 0.7656 (t70) cc_final: 0.7336 (t0) REVERT: C 456 LEU cc_start: 0.9155 (tp) cc_final: 0.8814 (tt) REVERT: C 587 MET cc_start: 0.8808 (mtp) cc_final: 0.8279 (mtp) REVERT: H 47 TRP cc_start: 0.8110 (t60) cc_final: 0.7749 (t60) REVERT: H 112 GLN cc_start: 0.7123 (pm20) cc_final: 0.6723 (pm20) REVERT: I 5 GLN cc_start: 0.8821 (mt0) cc_final: 0.8526 (tp40) REVERT: I 10 GLU cc_start: 0.6923 (mm-30) cc_final: 0.6641 (mm-30) REVERT: I 36 TRP cc_start: 0.7574 (m100) cc_final: 0.7069 (m-10) REVERT: I 47 TRP cc_start: 0.8073 (t60) cc_final: 0.7568 (t60) REVERT: I 65 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8092 (mmtt) REVERT: I 95 TYR cc_start: 0.6627 (m-80) cc_final: 0.6298 (m-80) REVERT: J 3 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7957 (tm-30) REVERT: J 47 TRP cc_start: 0.7756 (t60) cc_final: 0.7428 (t60) REVERT: J 51 ILE cc_start: 0.9042 (tt) cc_final: 0.8796 (tp) REVERT: J 73 ASP cc_start: 0.7988 (t0) cc_final: 0.7729 (t0) REVERT: J 80 TYR cc_start: 0.7651 (m-80) cc_final: 0.7215 (m-10) REVERT: J 95 TYR cc_start: 0.6723 (m-80) cc_final: 0.6426 (m-80) REVERT: L 79 GLN cc_start: 0.7327 (pt0) cc_final: 0.7115 (tm-30) REVERT: L 91 TYR cc_start: 0.8407 (p90) cc_final: 0.8064 (p90) REVERT: M 91 TYR cc_start: 0.8590 (p90) cc_final: 0.8385 (p90) REVERT: N 30 ASN cc_start: 0.8928 (t0) cc_final: 0.8695 (t0) REVERT: N 37 GLN cc_start: 0.6886 (tt0) cc_final: 0.6632 (tm-30) REVERT: N 69 LYS cc_start: 0.7597 (mtpp) cc_final: 0.7376 (mtpp) outliers start: 33 outliers final: 19 residues processed: 285 average time/residue: 0.3011 time to fit residues: 133.2443 Evaluate side-chains 247 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 228 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 106 TRP Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain N residue 28 HIS Chi-restraints excluded: chain N residue 70 ASP 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: 5.9990 chunk 179 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 232 optimal weight: 30.0000 chunk 192 optimal weight: 7.9990 chunk 213 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN ** I 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 19683 Z= 0.525 Angle : 0.715 13.668 26748 Z= 0.381 Chirality : 0.047 0.187 2907 Planarity : 0.005 0.057 3456 Dihedral : 5.458 23.712 2688 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.70 % Allowed : 11.58 % Favored : 85.72 % 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: -1.50 (0.16), residues: 2385 helix: 0.25 (0.28), residues: 333 sheet: -1.24 (0.17), residues: 786 loop : -1.10 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 35 HIS 0.011 0.001 HIS A 516 PHE 0.019 0.002 PHE B 294 TYR 0.038 0.002 TYR A 653 ARG 0.005 0.001 ARG N 18 *********************** 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 284 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 228 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8028 (mpp) REVERT: H 47 TRP cc_start: 0.8267 (t60) cc_final: 0.7947 (t60) REVERT: H 95 TYR cc_start: 0.6701 (m-80) cc_final: 0.6380 (m-80) REVERT: H 110 TRP cc_start: 0.8631 (OUTLIER) cc_final: 0.7279 (m-10) REVERT: H 112 GLN cc_start: 0.6670 (pm20) cc_final: 0.6419 (pm20) REVERT: I 65 LYS cc_start: 0.8568 (mmtt) cc_final: 0.8285 (mmtp) REVERT: I 80 TYR cc_start: 0.7631 (m-80) cc_final: 0.7402 (m-80) REVERT: J 5 GLN cc_start: 0.9003 (mt0) cc_final: 0.8775 (tm-30) REVERT: J 27 TYR cc_start: 0.6650 (p90) cc_final: 0.6290 (p90) REVERT: J 112 GLN cc_start: 0.6788 (pm20) cc_final: 0.6472 (pm20) REVERT: L 37 GLN cc_start: 0.7143 (tt0) cc_final: 0.6493 (tm-30) REVERT: L 79 GLN cc_start: 0.7367 (pt0) cc_final: 0.7126 (tm-30) REVERT: L 91 TYR cc_start: 0.8558 (p90) cc_final: 0.8166 (p90) REVERT: M 37 GLN cc_start: 0.7181 (tt0) cc_final: 0.6753 (tm-30) REVERT: M 91 TYR cc_start: 0.8582 (p90) cc_final: 0.8170 (p90) REVERT: N 37 GLN cc_start: 0.6973 (tt0) cc_final: 0.6645 (tm-30) outliers start: 56 outliers final: 26 residues processed: 263 average time/residue: 0.2858 time to fit residues: 117.1188 Evaluate side-chains 242 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 214 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 596 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 110 TRP Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 106 TRP Chi-restraints excluded: chain J residue 110 TRP Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain N residue 4 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 216 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 205 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN B 507 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 ASN N 30 ASN N 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19683 Z= 0.199 Angle : 0.569 9.425 26748 Z= 0.299 Chirality : 0.042 0.149 2907 Planarity : 0.004 0.044 3456 Dihedral : 4.958 20.961 2688 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.41 % Allowed : 13.51 % Favored : 84.08 % 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: -1.24 (0.17), residues: 2385 helix: 1.06 (0.29), residues: 315 sheet: -1.07 (0.16), residues: 819 loop : -1.08 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 36 HIS 0.005 0.001 HIS B 637 PHE 0.016 0.001 PHE C 194 TYR 0.029 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 283 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 233 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 HIS cc_start: 0.7670 (p90) cc_final: 0.7149 (p90) REVERT: A 421 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8051 (mpp) REVERT: C 177 HIS cc_start: 0.7784 (p90) cc_final: 0.7529 (p90) REVERT: C 178 ARG cc_start: 0.7899 (mtt90) cc_final: 0.7646 (mtt90) REVERT: H 47 TRP cc_start: 0.8205 (t60) cc_final: 0.7929 (t60) REVERT: I 10 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6355 (mm-30) REVERT: I 65 LYS cc_start: 0.8479 (mmtt) cc_final: 0.8255 (mmtt) REVERT: I 95 TYR cc_start: 0.6518 (m-80) cc_final: 0.6243 (m-80) REVERT: I 112 GLN cc_start: 0.6553 (pm20) cc_final: 0.6225 (pm20) REVERT: J 5 GLN cc_start: 0.8960 (mt0) cc_final: 0.8624 (tp40) REVERT: J 73 ASP cc_start: 0.7720 (t0) cc_final: 0.7252 (t0) REVERT: J 80 TYR cc_start: 0.7960 (m-80) cc_final: 0.7093 (m-10) REVERT: L 37 GLN cc_start: 0.7171 (tt0) cc_final: 0.6539 (tm-30) REVERT: L 87 TYR cc_start: 0.7284 (m-80) cc_final: 0.7041 (m-80) REVERT: M 37 GLN cc_start: 0.7157 (tt0) cc_final: 0.6744 (tm-30) REVERT: M 91 TYR cc_start: 0.8608 (p90) cc_final: 0.8191 (p90) REVERT: N 37 GLN cc_start: 0.7078 (tt0) cc_final: 0.6727 (tm-30) REVERT: N 61 ARG cc_start: 0.7454 (ptt180) cc_final: 0.6940 (ptt90) outliers start: 50 outliers final: 30 residues processed: 268 average time/residue: 0.3138 time to fit residues: 131.6232 Evaluate side-chains 249 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 218 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 596 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 106 TRP Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain N residue 70 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 205 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** H 5 GLN I 82 GLN L 30 ASN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 19683 Z= 0.450 Angle : 0.647 9.326 26748 Z= 0.342 Chirality : 0.044 0.176 2907 Planarity : 0.004 0.048 3456 Dihedral : 5.162 24.493 2688 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.09 % Allowed : 14.86 % Favored : 82.05 % 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: -1.36 (0.17), residues: 2385 helix: 0.85 (0.29), residues: 315 sheet: -1.27 (0.16), residues: 861 loop : -1.00 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP I 36 HIS 0.009 0.001 HIS A 516 PHE 0.026 0.002 PHE C 194 TYR 0.043 0.002 TYR A 653 ARG 0.003 0.000 ARG A 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 289 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 225 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 HIS cc_start: 0.7469 (p90) cc_final: 0.7252 (p90) REVERT: A 421 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8084 (mpp) REVERT: B 534 HIS cc_start: 0.8795 (OUTLIER) cc_final: 0.7992 (t-90) REVERT: B 627 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8401 (mtt180) REVERT: H 47 TRP cc_start: 0.8267 (t60) cc_final: 0.7948 (t60) REVERT: H 81 MET cc_start: 0.7307 (ttp) cc_final: 0.7016 (tpp) REVERT: H 95 TYR cc_start: 0.6537 (m-80) cc_final: 0.5739 (m-80) REVERT: I 10 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6315 (mm-30) REVERT: I 95 TYR cc_start: 0.6628 (m-80) cc_final: 0.5997 (m-80) REVERT: J 3 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7979 (mp10) REVERT: J 73 ASP cc_start: 0.7827 (t0) cc_final: 0.7389 (t0) REVERT: J 80 TYR cc_start: 0.7838 (m-80) cc_final: 0.7138 (m-10) REVERT: M 91 TYR cc_start: 0.8641 (p90) cc_final: 0.8146 (p90) REVERT: N 37 GLN cc_start: 0.7142 (tt0) cc_final: 0.6768 (tm-30) REVERT: N 61 ARG cc_start: 0.7551 (ptt180) cc_final: 0.7165 (ptt90) outliers start: 64 outliers final: 42 residues processed: 263 average time/residue: 0.2994 time to fit residues: 122.0483 Evaluate side-chains 262 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 627 ARG Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 529 CYS Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 596 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 106 TRP Chi-restraints excluded: chain J residue 110 TRP Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain M residue 28 HIS Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain N residue 4 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 0.9990 chunk 206 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 229 optimal weight: 7.9990 chunk 190 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19683 Z= 0.207 Angle : 0.570 10.973 26748 Z= 0.301 Chirality : 0.042 0.170 2907 Planarity : 0.004 0.040 3456 Dihedral : 4.864 23.643 2688 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.75 % Allowed : 16.06 % Favored : 81.19 % 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: -1.14 (0.17), residues: 2385 helix: 1.11 (0.29), residues: 315 sheet: -1.14 (0.16), residues: 858 loop : -0.88 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP I 36 HIS 0.013 0.001 HIS M 28 PHE 0.020 0.001 PHE C 194 TYR 0.035 0.001 TYR A 653 ARG 0.008 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 286 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 229 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 HIS cc_start: 0.7504 (p90) cc_final: 0.7277 (p90) REVERT: A 421 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8087 (mpp) REVERT: B 534 HIS cc_start: 0.8699 (OUTLIER) cc_final: 0.7863 (t-90) REVERT: C 177 HIS cc_start: 0.7884 (p90) cc_final: 0.7639 (p90) REVERT: C 421 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8208 (mpp) REVERT: C 534 HIS cc_start: 0.8768 (OUTLIER) cc_final: 0.7660 (t-90) REVERT: H 36 TRP cc_start: 0.6033 (m-10) cc_final: 0.5662 (m-10) REVERT: H 112 GLN cc_start: 0.6950 (pm20) cc_final: 0.6710 (pm20) REVERT: I 10 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6288 (mm-30) REVERT: I 112 GLN cc_start: 0.8016 (mp10) cc_final: 0.7340 (pm20) REVERT: J 73 ASP cc_start: 0.7845 (t0) cc_final: 0.7376 (t0) REVERT: J 80 TYR cc_start: 0.7832 (m-80) cc_final: 0.7172 (m-10) REVERT: L 87 TYR cc_start: 0.7126 (m-80) cc_final: 0.6905 (m-80) REVERT: M 37 GLN cc_start: 0.7168 (tt0) cc_final: 0.6306 (tm-30) REVERT: M 91 TYR cc_start: 0.8657 (p90) cc_final: 0.8233 (p90) REVERT: N 37 GLN cc_start: 0.7141 (tt0) cc_final: 0.6770 (tm-30) REVERT: N 61 ARG cc_start: 0.7595 (ptt180) cc_final: 0.7159 (ptt90) REVERT: N 89 GLN cc_start: 0.7646 (tp40) cc_final: 0.7369 (tp40) outliers start: 57 outliers final: 35 residues processed: 267 average time/residue: 0.2930 time to fit residues: 121.9068 Evaluate side-chains 259 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 220 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 529 CYS Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 106 TRP Chi-restraints excluded: chain N residue 69 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 193 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 228 optimal weight: 20.0000 chunk 142 optimal weight: 7.9990 chunk 139 optimal weight: 0.5980 chunk 105 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN N 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19683 Z= 0.313 Angle : 0.596 10.605 26748 Z= 0.314 Chirality : 0.043 0.155 2907 Planarity : 0.004 0.040 3456 Dihedral : 4.882 24.539 2688 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.94 % Allowed : 16.45 % Favored : 80.61 % 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: -1.15 (0.17), residues: 2385 helix: 1.09 (0.29), residues: 315 sheet: -1.08 (0.17), residues: 834 loop : -0.95 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP I 36 HIS 0.006 0.001 HIS A 516 PHE 0.021 0.002 PHE C 194 TYR 0.031 0.001 TYR A 653 ARG 0.007 0.000 ARG C 178 *********************** 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 281 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 220 time to evaluate : 2.346 Fit side-chains revert: symmetry clash REVERT: A 177 HIS cc_start: 0.7515 (p90) cc_final: 0.7179 (p90) REVERT: A 421 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8100 (mpp) REVERT: B 534 HIS cc_start: 0.8725 (OUTLIER) cc_final: 0.7871 (t-90) REVERT: B 627 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8423 (mtt180) REVERT: C 177 HIS cc_start: 0.7893 (p90) cc_final: 0.7662 (p90) REVERT: C 421 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8184 (mpp) REVERT: C 534 HIS cc_start: 0.8774 (OUTLIER) cc_final: 0.7648 (t-90) REVERT: H 112 GLN cc_start: 0.7042 (pm20) cc_final: 0.6760 (pm20) REVERT: I 10 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6306 (mm-30) REVERT: I 36 TRP cc_start: 0.5947 (m-10) cc_final: 0.5728 (m-10) REVERT: I 80 TYR cc_start: 0.7601 (m-80) cc_final: 0.7360 (m-10) REVERT: I 95 TYR cc_start: 0.6603 (m-80) cc_final: 0.6198 (m-80) REVERT: I 112 GLN cc_start: 0.8005 (mp10) cc_final: 0.7321 (pm20) REVERT: J 27 TYR cc_start: 0.6653 (p90) cc_final: 0.6438 (p90) REVERT: J 73 ASP cc_start: 0.7823 (t0) cc_final: 0.7478 (t0) REVERT: J 80 TYR cc_start: 0.7773 (m-80) cc_final: 0.7275 (m-10) REVERT: L 3 GLN cc_start: 0.8767 (tp40) cc_final: 0.8501 (mm110) REVERT: M 91 TYR cc_start: 0.8669 (p90) cc_final: 0.8141 (p90) REVERT: N 37 GLN cc_start: 0.7163 (tt0) cc_final: 0.6623 (tm-30) REVERT: N 61 ARG cc_start: 0.7629 (ptt180) cc_final: 0.7096 (ptt90) REVERT: N 89 GLN cc_start: 0.7641 (tp40) cc_final: 0.7302 (tp40) outliers start: 61 outliers final: 40 residues processed: 259 average time/residue: 0.3017 time to fit residues: 121.0008 Evaluate side-chains 262 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 627 ARG Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 106 TRP Chi-restraints excluded: chain M residue 23 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 0.0870 chunk 91 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 21 optimal weight: 0.0470 chunk 179 optimal weight: 0.9990 chunk 207 optimal weight: 20.0000 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN N 30 ASN N 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19683 Z= 0.163 Angle : 0.550 9.796 26748 Z= 0.290 Chirality : 0.041 0.175 2907 Planarity : 0.004 0.045 3456 Dihedral : 4.577 24.395 2688 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.51 % Allowed : 17.12 % Favored : 80.37 % 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: -1.01 (0.17), residues: 2385 helix: 1.34 (0.30), residues: 315 sheet: -1.05 (0.17), residues: 843 loop : -0.84 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP I 36 HIS 0.004 0.001 HIS A 637 PHE 0.015 0.001 PHE C 194 TYR 0.028 0.001 TYR A 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 288 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 236 time to evaluate : 1.939 Fit side-chains revert: symmetry clash REVERT: A 177 HIS cc_start: 0.7535 (p90) cc_final: 0.7117 (p90) REVERT: A 421 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8180 (mpp) REVERT: B 534 HIS cc_start: 0.8610 (OUTLIER) cc_final: 0.7688 (t-90) REVERT: C 177 HIS cc_start: 0.7899 (p90) cc_final: 0.7663 (p90) REVERT: C 421 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8245 (mpp) REVERT: C 534 HIS cc_start: 0.8568 (OUTLIER) cc_final: 0.7363 (t-90) REVERT: H 112 GLN cc_start: 0.7034 (pm20) cc_final: 0.6791 (pm20) REVERT: I 10 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6238 (mm-30) REVERT: I 80 TYR cc_start: 0.7486 (m-80) cc_final: 0.7268 (m-80) REVERT: I 112 GLN cc_start: 0.8023 (mp10) cc_final: 0.7422 (pm20) REVERT: J 73 ASP cc_start: 0.7812 (t0) cc_final: 0.7602 (t0) REVERT: L 3 GLN cc_start: 0.8766 (tp40) cc_final: 0.8558 (mm110) REVERT: M 91 TYR cc_start: 0.8644 (p90) cc_final: 0.8375 (p90) REVERT: N 37 GLN cc_start: 0.7186 (tt0) cc_final: 0.6798 (tm-30) REVERT: N 61 ARG cc_start: 0.7492 (ptt180) cc_final: 0.7006 (ptt90) REVERT: N 87 TYR cc_start: 0.7591 (m-10) cc_final: 0.7384 (m-10) REVERT: N 89 GLN cc_start: 0.7618 (tp40) cc_final: 0.7319 (tp40) outliers start: 52 outliers final: 30 residues processed: 270 average time/residue: 0.2861 time to fit residues: 120.3925 Evaluate side-chains 255 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 221 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 106 TRP Chi-restraints excluded: chain M residue 23 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 20.0000 chunk 199 optimal weight: 2.9990 chunk 212 optimal weight: 20.0000 chunk 128 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 65 optimal weight: 0.0980 chunk 192 optimal weight: 8.9990 chunk 201 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN N 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4092 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= 0.301 Angle : 0.591 11.357 26748 Z= 0.311 Chirality : 0.042 0.223 2907 Planarity : 0.004 0.051 3456 Dihedral : 4.710 23.229 2688 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.51 % Allowed : 17.32 % Favored : 80.17 % 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: -1.03 (0.17), residues: 2385 helix: 1.22 (0.29), residues: 315 sheet: -1.05 (0.17), residues: 819 loop : -0.84 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP I 36 HIS 0.006 0.001 HIS A 516 PHE 0.017 0.001 PHE A 294 TYR 0.050 0.001 TYR C 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 276 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 224 time to evaluate : 2.437 Fit side-chains revert: symmetry clash REVERT: A 177 HIS cc_start: 0.7532 (p90) cc_final: 0.7032 (p90) REVERT: B 534 HIS cc_start: 0.8676 (OUTLIER) cc_final: 0.7772 (t-90) REVERT: B 627 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7773 (mtm180) REVERT: C 178 ARG cc_start: 0.7894 (mtt90) cc_final: 0.7516 (mtm-85) REVERT: C 384 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.7835 (m-80) REVERT: C 421 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8214 (mpp) REVERT: C 534 HIS cc_start: 0.8718 (OUTLIER) cc_final: 0.7552 (t-90) REVERT: H 112 GLN cc_start: 0.7075 (pm20) cc_final: 0.6808 (pm20) REVERT: I 10 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6295 (mm-30) REVERT: I 27 TYR cc_start: 0.6420 (p90) cc_final: 0.6034 (p90) REVERT: I 80 TYR cc_start: 0.7470 (m-80) cc_final: 0.7195 (m-80) REVERT: J 112 GLN cc_start: 0.7072 (pm20) cc_final: 0.6812 (pm20) REVERT: L 3 GLN cc_start: 0.8771 (tp40) cc_final: 0.8558 (mm110) REVERT: M 91 TYR cc_start: 0.8674 (p90) cc_final: 0.8102 (p90) REVERT: N 37 GLN cc_start: 0.7263 (tt0) cc_final: 0.6880 (tm-30) REVERT: N 61 ARG cc_start: 0.7656 (ptt180) cc_final: 0.7086 (ptt90) REVERT: N 89 GLN cc_start: 0.7618 (tp40) cc_final: 0.7257 (tp40) outliers start: 52 outliers final: 42 residues processed: 258 average time/residue: 0.2859 time to fit residues: 114.2391 Evaluate side-chains 266 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 219 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 627 ARG Chi-restraints excluded: chain B residue 637 HIS Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 384 PHE Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 106 TRP Chi-restraints excluded: chain J residue 110 TRP Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain N residue 4 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 236 optimal weight: 0.7980 chunk 217 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 115 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN N 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19683 Z= 0.186 Angle : 0.567 11.496 26748 Z= 0.296 Chirality : 0.042 0.214 2907 Planarity : 0.004 0.064 3456 Dihedral : 4.602 24.133 2688 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.32 % Allowed : 17.90 % Favored : 79.79 % 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: -0.98 (0.17), residues: 2385 helix: 1.35 (0.30), residues: 315 sheet: -1.04 (0.16), residues: 858 loop : -0.80 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP J 36 HIS 0.004 0.001 HIS C 637 PHE 0.016 0.001 PHE A 294 TYR 0.030 0.001 TYR A 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 267 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 219 time to evaluate : 2.291 Fit side-chains revert: symmetry clash REVERT: A 177 HIS cc_start: 0.7529 (p90) cc_final: 0.7003 (p90) REVERT: A 421 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8172 (mpp) REVERT: B 534 HIS cc_start: 0.8609 (OUTLIER) cc_final: 0.7662 (t-90) REVERT: C 384 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: C 421 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8217 (mpp) REVERT: C 534 HIS cc_start: 0.8613 (OUTLIER) cc_final: 0.7421 (t-90) REVERT: I 10 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6289 (mm-30) REVERT: I 27 TYR cc_start: 0.6441 (p90) cc_final: 0.6105 (p90) REVERT: I 80 TYR cc_start: 0.7506 (m-80) cc_final: 0.7252 (m-80) REVERT: I 112 GLN cc_start: 0.7937 (mp10) cc_final: 0.7312 (pm20) REVERT: J 112 GLN cc_start: 0.7120 (pm20) cc_final: 0.6856 (pm20) REVERT: M 91 TYR cc_start: 0.8665 (p90) cc_final: 0.8091 (p90) REVERT: N 61 ARG cc_start: 0.7549 (ptt180) cc_final: 0.7158 (ptt90) REVERT: N 89 GLN cc_start: 0.7606 (tp40) cc_final: 0.7250 (tp40) outliers start: 48 outliers final: 37 residues processed: 250 average time/residue: 0.2890 time to fit residues: 112.4665 Evaluate side-chains 256 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 214 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 637 HIS Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 384 PHE Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 106 TRP Chi-restraints excluded: chain J residue 110 TRP Chi-restraints excluded: chain M residue 23 CYS 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: 4.9990 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 188 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 165 optimal weight: 0.0060 chunk 10 optimal weight: 2.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN I 5 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.089681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.060896 restraints weight = 51103.168| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.22 r_work: 0.2812 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4268 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= 0.204 Angle : 0.556 9.906 26748 Z= 0.291 Chirality : 0.041 0.173 2907 Planarity : 0.004 0.053 3456 Dihedral : 4.543 22.934 2688 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.65 % Allowed : 17.32 % Favored : 80.03 % 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: -0.84 (0.17), residues: 2385 helix: 1.41 (0.30), residues: 315 sheet: -0.86 (0.17), residues: 822 loop : -0.78 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP J 36 HIS 0.004 0.001 HIS A 516 PHE 0.015 0.001 PHE C 194 TYR 0.028 0.001 TYR A 653 ARG 0.008 0.000 ARG C 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4152.36 seconds wall clock time: 75 minutes 51.69 seconds (4551.69 seconds total)