Starting phenix.real_space_refine on Tue Apr 9 17:06:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxi_27058/04_2024/8cxi_27058.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxi_27058/04_2024/8cxi_27058.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/8cxi_27058/04_2024/8cxi_27058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxi_27058/04_2024/8cxi_27058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxi_27058/04_2024/8cxi_27058.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxi_27058/04_2024/8cxi_27058.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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 98 atoms to isotropic. 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 114 5.16 5 C 10612 2.51 5 N 2902 2.21 5 O 3204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 57": "NH1" <-> "NH2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A ARG 94": "NH1" <-> "NH2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A ARG 292": "NH1" <-> "NH2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 10": "NH1" <-> "NH2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B ARG 299": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "E ARG 10": "NH1" <-> "NH2" Residue "E ARG 23": "NH1" <-> "NH2" Residue "E ARG 31": "NH1" <-> "NH2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "h ARG 19": "NH1" <-> "NH2" Residue "l PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 81": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ARG 94": "NH1" <-> "NH2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C ARG 299": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C ARG 402": "NH1" <-> "NH2" Residue "F ARG 10": "NH1" <-> "NH2" Residue "F GLU 21": "OE1" <-> "OE2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 31": "NH1" <-> "NH2" Residue "F ARG 38": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16832 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3790 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "D" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "H" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1036 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 761 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "B" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3790 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "h" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1024 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "l" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 743 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "C" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3790 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "F" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.83, per 1000 atoms: 0.52 Number of scatterers: 16832 At special positions: 0 Unit cell: (106, 203.52, 121.9, 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 114 16.00 O 3204 8.00 N 2902 7.00 C 10612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.95 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.31 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 291 " distance=2.02 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 339 " distance=1.90 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 105 " distance=0.96 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 116 " distance=2.04 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.82 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.05 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 190 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 308 " - pdb=" SG CYS C 339 " distance=2.93 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 Atom "HETATM16746 O5 NAG G 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " BETA1-6 " NAG G 1 " - " FUC G 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 4 " NAG-ASN " NAG G 1 " - " ASN A 154 " Time building additional restraints: 6.75 Conformation dependent library (CDL) restraints added in 3.0 seconds 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3948 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 40 sheets defined 23.0% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 263 through 269 Processing helix chain 'A' and resid 405 through 425 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 437 through 457 Processing helix chain 'A' and resid 461 through 478 Processing helix chain 'A' and resid 483 through 499 removed outlier: 3.535A pdb=" N GLY A 492 " --> pdb=" O CYS A 488 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 498 " --> pdb=" O VAL A 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 11 Processing helix chain 'D' and resid 23 through 39 Processing helix chain 'D' and resid 41 through 53 removed outlier: 3.563A pdb=" N LEU D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 97 through 100B removed outlier: 4.058A pdb=" N TYR H 100A" --> pdb=" O VAL H 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 27C through 32 removed outlier: 3.930A pdb=" N ASN L 31 " --> pdb=" O ALA L 27C" (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU L 32 " --> pdb=" O ASP L 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 27C through 32' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 82 through 87 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.985A pdb=" N ILE B 152 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 162 removed outlier: 3.923A pdb=" N GLU B 162 " --> pdb=" O HIS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 220 Processing helix chain 'B' and resid 261 through 269 removed outlier: 3.781A pdb=" N VAL B 265 " --> pdb=" O GLN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 425 Processing helix chain 'B' and resid 426 through 429 Processing helix chain 'B' and resid 437 through 457 Processing helix chain 'B' and resid 463 through 478 Processing helix chain 'B' and resid 482 through 500 Processing helix chain 'E' and resid 6 through 11 removed outlier: 3.956A pdb=" N THR E 9 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 39 Processing helix chain 'E' and resid 40 through 52 removed outlier: 3.910A pdb=" N LEU E 44 " --> pdb=" O PRO E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 71 removed outlier: 3.553A pdb=" N LYS E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 32 Processing helix chain 'h' and resid 83 through 87 removed outlier: 3.508A pdb=" N ASP h 86 " --> pdb=" O THR h 83 " (cutoff:3.500A) Processing helix chain 'l' and resid 28 through 33 Processing helix chain 'l' and resid 79 through 83 removed outlier: 3.605A pdb=" N GLU l 83 " --> pdb=" O PRO l 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.872A pdb=" N SER C 86 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 269 Processing helix chain 'C' and resid 405 through 425 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 437 through 457 Processing helix chain 'C' and resid 463 through 479 Processing helix chain 'C' and resid 483 through 500 removed outlier: 3.566A pdb=" N LEU C 498 " --> pdb=" O VAL C 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 11 removed outlier: 3.604A pdb=" N LYS F 11 " --> pdb=" O SER F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 39 Processing helix chain 'F' and resid 40 through 52 Processing helix chain 'F' and resid 56 through 74 removed outlier: 3.702A pdb=" N LYS F 60 " --> pdb=" O SER F 56 " (cutoff:3.500A) Proline residue: F 72 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.684A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N MET A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 12 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N HIS A 210 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N MET A 125 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER A 58 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 127 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 54 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.684A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N MET A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 12 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG A 138 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR A 48 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU A 136 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 21 through 26 removed outlier: 4.511A pdb=" N LYS A 290 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 63 through 65 removed outlier: 3.982A pdb=" N SER A 112 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 63 through 65 Processing sheet with id=AA6, first strand: chain 'A' and resid 243 through 247 Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 313 Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 313 Processing sheet with id=AA9, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AB1, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.587A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.587A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.399A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AB6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB7, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.716A pdb=" N ASP B 10 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR B 48 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS B 281 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 276 " --> pdb=" O ARG B 283 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS B 210 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA B 54 " --> pdb=" O SER B 129 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.716A pdb=" N ASP B 10 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG B 138 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR B 48 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU B 136 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 21 through 26 removed outlier: 5.434A pdb=" N ASP B 296 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N SER B 185 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 58 through 59 Processing sheet with id=AC2, first strand: chain 'B' and resid 63 through 72 removed outlier: 6.411A pdb=" N LYS B 118 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N MET B 68 " --> pdb=" O CYS B 116 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS B 116 " --> pdb=" O MET B 68 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER B 70 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 114 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER B 72 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER B 112 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 243 through 247 Processing sheet with id=AC4, first strand: chain 'B' and resid 312 through 320 removed outlier: 7.088A pdb=" N THR B 315 " --> pdb=" O GLN B 331 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N GLN B 331 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE B 317 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU B 329 " --> pdb=" O ILE B 317 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 339 through 340 removed outlier: 3.859A pdb=" N CYS B 339 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 365 " --> pdb=" O CYS B 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 343 through 346 Processing sheet with id=AC7, first strand: chain 'h' and resid 3 through 7 removed outlier: 3.635A pdb=" N GLN h 3 " --> pdb=" O SER h 25 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER h 25 " --> pdb=" O GLN h 3 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'h' and resid 11 through 12 removed outlier: 3.555A pdb=" N TRP h 33 " --> pdb=" O ASP h 95 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N MET h 34 " --> pdb=" O ARG h 50 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP h 36 " --> pdb=" O VAL h 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'h' and resid 11 through 12 removed outlier: 4.509A pdb=" N VAL h 102 " --> pdb=" O ARG h 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'l' and resid 9 through 12 removed outlier: 7.123A pdb=" N VAL l 11 " --> pdb=" O THR l 105 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TRP l 35 " --> pdb=" O MET l 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'l' and resid 9 through 12 removed outlier: 7.123A pdb=" N VAL l 11 " --> pdb=" O THR l 105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'l' and resid 19 through 23 Processing sheet with id=AD4, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.606A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N MET C 34 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL C 12 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N HIS C 210 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY C 127 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C 54 " --> pdb=" O SER C 129 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.606A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N MET C 34 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL C 12 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG C 138 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR C 48 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLU C 136 " --> pdb=" O THR C 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 20 through 26 Processing sheet with id=AD7, first strand: chain 'C' and resid 63 through 65 Processing sheet with id=AD8, first strand: chain 'C' and resid 63 through 65 Processing sheet with id=AD9, first strand: chain 'C' and resid 243 through 246 Processing sheet with id=AE1, first strand: chain 'C' and resid 312 through 314 Processing sheet with id=AE2, first strand: chain 'C' and resid 312 through 314 Processing sheet with id=AE3, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AE4, first strand: chain 'C' and resid 343 through 346 753 hydrogen bonds defined for protein. 1968 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: 6.31 Time building geometry restraints manager: 7.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 2730 1.27 - 1.41: 4286 1.41 - 1.54: 9975 1.54 - 1.68: 26 1.68 - 1.81: 179 Bond restraints: 17196 Sorted by residual: bond pdb=" CA SER C 72 " pdb=" C SER C 72 " ideal model delta sigma weight residual 1.520 1.415 0.105 1.20e-02 6.94e+03 7.65e+01 bond pdb=" CA MET A 125 " pdb=" C MET A 125 " ideal model delta sigma weight residual 1.522 1.425 0.098 1.19e-02 7.06e+03 6.78e+01 bond pdb=" C ARG C 73 " pdb=" O ARG C 73 " ideal model delta sigma weight residual 1.234 1.139 0.095 1.20e-02 6.94e+03 6.27e+01 bond pdb=" C MET A 125 " pdb=" O MET A 125 " ideal model delta sigma weight residual 1.235 1.146 0.089 1.23e-02 6.61e+03 5.26e+01 bond pdb=" CA LYS A 316 " pdb=" C LYS A 316 " ideal model delta sigma weight residual 1.522 1.426 0.095 1.37e-02 5.33e+03 4.83e+01 ... (remaining 17191 not shown) Histogram of bond angle deviations from ideal: 94.59 - 102.77: 116 102.77 - 110.95: 6778 110.95 - 119.13: 7479 119.13 - 127.32: 8702 127.32 - 135.50: 229 Bond angle restraints: 23304 Sorted by residual: angle pdb=" C CYS B 74 " pdb=" N PRO B 75 " pdb=" CA PRO B 75 " ideal model delta sigma weight residual 119.84 135.50 -15.66 1.25e+00 6.40e-01 1.57e+02 angle pdb=" N LYS A 316 " pdb=" CA LYS A 316 " pdb=" C LYS A 316 " ideal model delta sigma weight residual 113.23 100.07 13.16 1.24e+00 6.50e-01 1.13e+02 angle pdb=" N ARG B 73 " pdb=" CA ARG B 73 " pdb=" C ARG B 73 " ideal model delta sigma weight residual 112.92 125.37 -12.45 1.23e+00 6.61e-01 1.02e+02 angle pdb=" N THR A 315 " pdb=" CA THR A 315 " pdb=" C THR A 315 " ideal model delta sigma weight residual 111.40 123.14 -11.74 1.22e+00 6.72e-01 9.26e+01 angle pdb=" C CYS C 74 " pdb=" N PRO C 75 " pdb=" CA PRO C 75 " ideal model delta sigma weight residual 119.84 131.79 -11.95 1.25e+00 6.40e-01 9.14e+01 ... (remaining 23299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.85: 9746 24.85 - 49.70: 412 49.70 - 74.55: 51 74.55 - 99.40: 28 99.40 - 124.25: 2 Dihedral angle restraints: 10239 sinusoidal: 4036 harmonic: 6203 Sorted by residual: dihedral pdb=" CB CYS A 308 " pdb=" SG CYS A 308 " pdb=" SG CYS A 339 " pdb=" CB CYS A 339 " ideal model delta sinusoidal sigma weight residual -86.00 -168.58 82.58 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS A 3 " pdb=" SG CYS A 3 " pdb=" SG CYS A 30 " pdb=" CB CYS A 30 " ideal model delta sinusoidal sigma weight residual -86.00 -153.39 67.39 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS C 3 " pdb=" SG CYS C 3 " pdb=" SG CYS C 30 " pdb=" CB CYS C 30 " ideal model delta sinusoidal sigma weight residual -86.00 -152.73 66.73 1 1.00e+01 1.00e-02 5.81e+01 ... (remaining 10236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.648: 2640 0.648 - 1.296: 0 1.296 - 1.944: 0 1.944 - 2.592: 0 2.592 - 3.240: 1 Chirality restraints: 2641 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 154 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 0.84 -3.24 2.00e-01 2.50e+01 2.62e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.15e+01 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.04e+01 ... (remaining 2638 not shown) Planarity restraints: 2943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 154 " -0.031 2.00e-02 2.50e+03 2.51e-01 7.90e+02 pdb=" CG ASN A 154 " 0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN A 154 " -0.172 2.00e-02 2.50e+03 pdb=" ND2 ASN A 154 " 0.432 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.305 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 239 " -0.031 2.00e-02 2.50e+03 6.49e-02 4.22e+01 pdb=" C LYS C 239 " 0.112 2.00e-02 2.50e+03 pdb=" O LYS C 239 " -0.043 2.00e-02 2.50e+03 pdb=" N GLU C 240 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 1 " -0.024 2.00e-02 2.50e+03 4.85e-02 2.35e+01 pdb=" C ILE C 1 " 0.084 2.00e-02 2.50e+03 pdb=" O ILE C 1 " -0.032 2.00e-02 2.50e+03 pdb=" N ARG C 2 " -0.028 2.00e-02 2.50e+03 ... (remaining 2940 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.67: 10 1.67 - 2.47: 180 2.47 - 3.28: 18104 3.28 - 4.09: 39051 4.09 - 4.90: 71646 Warning: very small nonbonded interaction distances. Nonbonded interactions: 128991 Sorted by model distance: nonbonded pdb=" OD2 ASP B 10 " pdb=" NH2 ARG B 420 " model vdw 0.857 2.520 nonbonded pdb=" CD2 TYR l 36 " pdb=" CD2 LEU l 46 " model vdw 1.362 3.760 nonbonded pdb=" O PHE B 312 " pdb=" CD1 ILE B 396 " model vdw 1.364 3.460 nonbonded pdb=" CD2 LEU B 472 " pdb=" CE MET B 487 " model vdw 1.472 3.880 nonbonded pdb=" OG SER h 100J" pdb=" NE ARG C 73 " model vdw 1.517 2.520 ... (remaining 128986 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 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' } ncs_group { reference = (chain 'H' and (resid 1 through 100 or resid 100B through 112)) selection = chain 'h' } ncs_group { reference = (chain 'L' and resid 8 through 105) selection = chain 'l' } 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 4.250 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 45.890 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 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 0.105 17196 Z= 0.536 Angle : 0.969 15.659 23304 Z= 0.574 Chirality : 0.086 3.240 2641 Planarity : 0.006 0.099 2942 Dihedral : 14.268 124.253 6237 Min Nonbonded Distance : 0.857 Molprobity Statistics. All-atom Clashscore : 26.16 Ramachandran Plot: Outliers : 0.69 % Allowed : 9.57 % Favored : 89.74 % Rotamer: Outliers : 3.00 % Allowed : 9.45 % Favored : 87.55 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.16), residues: 2174 helix: -1.25 (0.21), residues: 450 sheet: -0.32 (0.19), residues: 733 loop : -3.08 (0.16), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 400 HIS 0.006 0.001 HIS A 235 PHE 0.016 0.002 PHE A 431 TYR 0.020 0.002 TYR A 61 ARG 0.011 0.001 ARG C 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 457 time to evaluate : 2.026 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: symmetry clash revert: symmetry clash REVERT: A 134 ASN cc_start: 0.8108 (p0) cc_final: 0.7795 (p0) REVERT: A 276 GLU cc_start: 0.6129 (pt0) cc_final: 0.5909 (pt0) REVERT: A 395 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7698 (ptpp) REVERT: A 495 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7944 (mp) REVERT: H 32 HIS cc_start: 0.6889 (m90) cc_final: 0.6579 (m90) REVERT: B 136 GLU cc_start: 0.6794 (tt0) cc_final: 0.5990 (tt0) REVERT: B 140 MET cc_start: 0.7585 (mmt) cc_final: 0.7324 (mmm) REVERT: B 247 ASP cc_start: 0.6537 (t0) cc_final: 0.6318 (t0) REVERT: B 429 TRP cc_start: 0.7361 (m100) cc_final: 0.7066 (m100) REVERT: E 14 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7886 (m) REVERT: E 38 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6522 (mmt90) REVERT: C 67 ASP cc_start: 0.8344 (p0) cc_final: 0.8042 (p0) REVERT: C 87 ASP cc_start: 0.7556 (t0) cc_final: 0.7133 (t0) REVERT: C 134 ASN cc_start: 0.8427 (p0) cc_final: 0.8064 (p0) outliers start: 54 outliers final: 19 residues processed: 497 average time/residue: 0.3155 time to fit residues: 228.4539 Evaluate side-chains 354 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 332 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 4.9990 chunk 164 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 110 optimal weight: 0.2980 chunk 87 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 65 optimal weight: 30.0000 chunk 103 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 197 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 HIS A 163 ASN A 235 HIS A 288 HIS ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN B 52 ASN B 85 GLN B 134 ASN B 163 ASN B 261 GLN B 344 GLN B 350 GLN ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 GLN E 7 HIS ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 HIS C 154 ASN ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 HIS C 350 GLN F 7 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17196 Z= 0.225 Angle : 0.762 19.320 23304 Z= 0.388 Chirality : 0.051 1.108 2641 Planarity : 0.006 0.154 2942 Dihedral : 11.338 110.757 2548 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.98 % Favored : 89.88 % Rotamer: Outliers : 3.67 % Allowed : 15.84 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.84 (0.17), residues: 2174 helix: 0.16 (0.25), residues: 429 sheet: -0.11 (0.19), residues: 700 loop : -2.71 (0.16), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 36 HIS 0.005 0.001 HIS B 210 PHE 0.036 0.002 PHE A 314 TYR 0.015 0.001 TYR D 25 ARG 0.006 0.001 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 350 time to evaluate : 1.912 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: A 90 TYR cc_start: 0.8491 (m-80) cc_final: 0.8273 (m-80) REVERT: A 151 MET cc_start: 0.6002 (mmm) cc_final: 0.5627 (mmm) REVERT: A 221 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.8041 (mt) REVERT: A 316 LYS cc_start: 0.6646 (tttt) cc_final: 0.5850 (tttp) REVERT: A 426 ASP cc_start: 0.5724 (m-30) cc_final: 0.5478 (m-30) REVERT: H 32 HIS cc_start: 0.6929 (m90) cc_final: 0.6707 (m90) REVERT: H 94 ARG cc_start: 0.6738 (ttp-170) cc_final: 0.6280 (ttp-170) REVERT: C 87 ASP cc_start: 0.7302 (t0) cc_final: 0.6825 (t0) REVERT: C 473 MET cc_start: 0.7110 (tpp) cc_final: 0.6848 (mmm) REVERT: C 487 MET cc_start: 0.6256 (OUTLIER) cc_final: 0.6003 (mmt) outliers start: 66 outliers final: 44 residues processed: 396 average time/residue: 0.2759 time to fit residues: 168.5596 Evaluate side-chains 370 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 324 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 487 MET Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 7.9990 chunk 61 optimal weight: 30.0000 chunk 164 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 197 optimal weight: 40.0000 chunk 213 optimal weight: 2.9990 chunk 175 optimal weight: 20.0000 chunk 195 optimal weight: 20.0000 chunk 67 optimal weight: 40.0000 chunk 158 optimal weight: 50.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS B 447 GLN h 35 HIS ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 HIS F 17 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17196 Z= 0.346 Angle : 0.749 17.091 23304 Z= 0.386 Chirality : 0.050 0.880 2641 Planarity : 0.005 0.103 2942 Dihedral : 10.629 99.783 2527 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.53 % Favored : 89.33 % Rotamer: Outliers : 5.11 % Allowed : 16.51 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -1.65 (0.17), residues: 2174 helix: 0.29 (0.26), residues: 429 sheet: 0.09 (0.20), residues: 670 loop : -2.58 (0.16), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 400 HIS 0.016 0.001 HIS C 288 PHE 0.029 0.002 PHE A 382 TYR 0.015 0.002 TYR D 25 ARG 0.005 0.000 ARG l 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 339 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8101 (mt) REVERT: A 345 MET cc_start: 0.6852 (mmm) cc_final: 0.6531 (mmm) REVERT: H 32 HIS cc_start: 0.6959 (m90) cc_final: 0.6673 (m90) REVERT: E 38 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7053 (mmt90) REVERT: C 87 ASP cc_start: 0.7408 (t0) cc_final: 0.7029 (t0) REVERT: C 125 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6539 (ttt) REVERT: C 473 MET cc_start: 0.7142 (tpp) cc_final: 0.6924 (mmm) outliers start: 92 outliers final: 57 residues processed: 397 average time/residue: 0.2579 time to fit residues: 159.9819 Evaluate side-chains 379 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 319 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 61 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 198 optimal weight: 30.0000 chunk 209 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 187 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 172 ASN A 465 GLN ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17196 Z= 0.289 Angle : 0.712 14.534 23304 Z= 0.365 Chirality : 0.048 0.802 2641 Planarity : 0.005 0.089 2942 Dihedral : 9.989 93.819 2525 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.95 % Favored : 88.96 % Rotamer: Outliers : 5.61 % Allowed : 17.23 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -1.56 (0.17), residues: 2174 helix: 0.28 (0.26), residues: 447 sheet: 0.21 (0.21), residues: 664 loop : -2.56 (0.16), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 400 HIS 0.003 0.001 HIS B 210 PHE 0.016 0.001 PHE F 42 TYR 0.013 0.002 TYR h 29 ARG 0.006 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 319 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.6341 (mmm) cc_final: 0.6062 (mmm) REVERT: A 221 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8053 (mt) REVERT: A 345 MET cc_start: 0.7156 (mmm) cc_final: 0.6772 (mmm) REVERT: H 32 HIS cc_start: 0.6955 (m90) cc_final: 0.6667 (m90) REVERT: H 94 ARG cc_start: 0.6724 (ttp-170) cc_final: 0.6247 (ttp-170) REVERT: E 38 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7074 (mmt90) REVERT: C 125 MET cc_start: 0.7111 (tpp) cc_final: 0.6823 (ttt) REVERT: C 191 GLU cc_start: 0.6301 (tp30) cc_final: 0.5039 (tp30) outliers start: 101 outliers final: 65 residues processed: 391 average time/residue: 0.2509 time to fit residues: 153.4718 Evaluate side-chains 377 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 310 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 156 optimal weight: 50.0000 chunk 86 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 144 optimal weight: 50.0000 chunk 0 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17196 Z= 0.281 Angle : 0.690 12.772 23304 Z= 0.353 Chirality : 0.048 0.783 2641 Planarity : 0.005 0.077 2942 Dihedral : 9.046 91.505 2523 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.04 % Favored : 88.82 % Rotamer: Outliers : 5.50 % Allowed : 18.84 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.05 % 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: -1.48 (0.18), residues: 2174 helix: 0.23 (0.25), residues: 459 sheet: 0.45 (0.21), residues: 634 loop : -2.55 (0.16), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 400 HIS 0.005 0.001 HIS C 210 PHE 0.018 0.002 PHE F 37 TYR 0.017 0.001 TYR h 79 ARG 0.004 0.000 ARG l 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 320 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.6320 (mmm) cc_final: 0.6080 (mmm) REVERT: A 375 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6543 (ttm) REVERT: A 382 PHE cc_start: 0.7865 (m-10) cc_final: 0.7496 (m-80) REVERT: D 25 TYR cc_start: 0.6561 (OUTLIER) cc_final: 0.4799 (p90) REVERT: H 11 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6592 (tp) REVERT: H 94 ARG cc_start: 0.6761 (ttp-170) cc_final: 0.6264 (ttp-170) REVERT: B 317 ILE cc_start: 0.7698 (pt) cc_final: 0.7489 (pt) REVERT: C 191 GLU cc_start: 0.6267 (tp30) cc_final: 0.4987 (tp30) REVERT: C 376 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7204 (pp) REVERT: C 473 MET cc_start: 0.7002 (tpp) cc_final: 0.6558 (tpt) outliers start: 99 outliers final: 74 residues processed: 391 average time/residue: 0.2564 time to fit residues: 157.5265 Evaluate side-chains 387 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 309 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 50.0000 chunk 188 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 209 optimal weight: 0.7980 chunk 174 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17196 Z= 0.304 Angle : 0.702 12.296 23304 Z= 0.359 Chirality : 0.048 0.774 2641 Planarity : 0.004 0.066 2942 Dihedral : 8.650 88.362 2517 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.22 % Favored : 88.64 % Rotamer: Outliers : 5.78 % Allowed : 19.18 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -1.41 (0.18), residues: 2174 helix: 0.20 (0.25), residues: 459 sheet: 0.31 (0.20), residues: 694 loop : -2.47 (0.17), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 400 HIS 0.003 0.001 HIS A 399 PHE 0.015 0.002 PHE F 42 TYR 0.012 0.002 TYR B 203 ARG 0.007 0.000 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 321 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.6507 (mmm) cc_final: 0.6263 (mmm) REVERT: A 475 LEU cc_start: 0.7985 (tt) cc_final: 0.7701 (tt) REVERT: D 25 TYR cc_start: 0.6739 (OUTLIER) cc_final: 0.5010 (p90) REVERT: H 11 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6591 (tp) REVERT: H 94 ARG cc_start: 0.6765 (ttp-170) cc_final: 0.6269 (ttp-170) REVERT: B 4 ILE cc_start: 0.7759 (mm) cc_final: 0.7553 (mm) REVERT: B 136 GLU cc_start: 0.6485 (tt0) cc_final: 0.6140 (tt0) REVERT: B 168 GLU cc_start: 0.6371 (mt-10) cc_final: 0.6086 (mt-10) REVERT: C 61 TYR cc_start: 0.8425 (p90) cc_final: 0.8092 (p90) REVERT: C 191 GLU cc_start: 0.6230 (tp30) cc_final: 0.4630 (tp30) REVERT: C 376 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7150 (pp) REVERT: C 456 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7989 (mp) outliers start: 104 outliers final: 86 residues processed: 389 average time/residue: 0.2641 time to fit residues: 158.4702 Evaluate side-chains 404 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 314 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 209 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17196 Z= 0.239 Angle : 0.667 11.318 23304 Z= 0.342 Chirality : 0.047 0.757 2641 Planarity : 0.004 0.055 2942 Dihedral : 8.348 85.543 2517 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.90 % Favored : 88.96 % Rotamer: Outliers : 5.39 % Allowed : 20.12 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.18), residues: 2174 helix: 0.28 (0.25), residues: 462 sheet: 0.42 (0.21), residues: 670 loop : -2.45 (0.17), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 400 HIS 0.004 0.001 HIS B 148 PHE 0.026 0.001 PHE E 37 TYR 0.010 0.001 TYR A 203 ARG 0.006 0.000 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 325 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.6519 (mmm) cc_final: 0.6308 (mmm) REVERT: D 25 TYR cc_start: 0.6399 (OUTLIER) cc_final: 0.4891 (p90) REVERT: B 136 GLU cc_start: 0.6457 (tt0) cc_final: 0.6030 (tt0) REVERT: B 168 GLU cc_start: 0.6378 (mt-10) cc_final: 0.5910 (mt-10) REVERT: h 82 LEU cc_start: 0.4493 (OUTLIER) cc_final: 0.3988 (tt) REVERT: C 61 TYR cc_start: 0.8290 (p90) cc_final: 0.8067 (p90) outliers start: 97 outliers final: 82 residues processed: 394 average time/residue: 0.2622 time to fit residues: 160.6472 Evaluate side-chains 395 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 311 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 3.9990 chunk 83 optimal weight: 0.3980 chunk 124 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 142 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 164 optimal weight: 9.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17196 Z= 0.222 Angle : 0.655 9.770 23304 Z= 0.334 Chirality : 0.046 0.754 2641 Planarity : 0.004 0.048 2942 Dihedral : 7.905 82.302 2515 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.53 % Favored : 89.33 % Rotamer: Outliers : 5.73 % Allowed : 20.51 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.18), residues: 2174 helix: 0.39 (0.25), residues: 459 sheet: 0.59 (0.21), residues: 657 loop : -2.49 (0.17), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 400 HIS 0.004 0.001 HIS B 148 PHE 0.021 0.001 PHE E 37 TYR 0.010 0.001 TYR A 203 ARG 0.007 0.000 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 317 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 TYR cc_start: 0.6102 (OUTLIER) cc_final: 0.4780 (p90) REVERT: H 11 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6505 (tp) REVERT: H 94 ARG cc_start: 0.6898 (ttp-170) cc_final: 0.6352 (ttp-170) REVERT: B 27 HIS cc_start: 0.8031 (OUTLIER) cc_final: 0.7244 (t-90) REVERT: B 136 GLU cc_start: 0.6400 (tt0) cc_final: 0.6030 (tt0) REVERT: B 168 GLU cc_start: 0.6370 (mt-10) cc_final: 0.5908 (mt-10) REVERT: l 47 MET cc_start: 0.5354 (mpp) cc_final: 0.4968 (ptp) REVERT: C 175 ARG cc_start: 0.5018 (ptt-90) cc_final: 0.4712 (ptp90) outliers start: 103 outliers final: 88 residues processed: 388 average time/residue: 0.2598 time to fit residues: 159.4782 Evaluate side-chains 397 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 306 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 153 optimal weight: 10.0000 chunk 59 optimal weight: 30.0000 chunk 176 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17196 Z= 0.302 Angle : 0.694 11.002 23304 Z= 0.357 Chirality : 0.048 0.752 2641 Planarity : 0.004 0.049 2942 Dihedral : 7.614 79.028 2515 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.95 % Favored : 88.87 % Rotamer: Outliers : 5.84 % Allowed : 20.51 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.33 (0.18), residues: 2174 helix: 0.30 (0.25), residues: 459 sheet: 0.35 (0.20), residues: 735 loop : -2.53 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 400 HIS 0.004 0.001 HIS B 148 PHE 0.022 0.002 PHE F 37 TYR 0.012 0.001 TYR A 203 ARG 0.007 0.000 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 318 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 MET cc_start: 0.7469 (mtp) cc_final: 0.7004 (mtt) REVERT: D 25 TYR cc_start: 0.6380 (OUTLIER) cc_final: 0.4971 (p90) REVERT: H 11 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6529 (tp) REVERT: B 27 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.7314 (t-90) REVERT: B 136 GLU cc_start: 0.6454 (tt0) cc_final: 0.6165 (tt0) REVERT: B 168 GLU cc_start: 0.6441 (mt-10) cc_final: 0.6068 (mt-10) REVERT: C 175 ARG cc_start: 0.5450 (ptt-90) cc_final: 0.5058 (ptp90) outliers start: 105 outliers final: 86 residues processed: 388 average time/residue: 0.2547 time to fit residues: 155.3174 Evaluate side-chains 400 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 311 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 143 optimal weight: 20.0000 chunk 216 optimal weight: 4.9990 chunk 198 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 39 GLN l 38 GLN C 103 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17196 Z= 0.209 Angle : 0.665 13.956 23304 Z= 0.339 Chirality : 0.047 0.747 2641 Planarity : 0.004 0.049 2942 Dihedral : 7.344 75.385 2515 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.44 % Favored : 89.37 % Rotamer: Outliers : 4.95 % Allowed : 21.85 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.28 (0.18), residues: 2174 helix: 0.45 (0.26), residues: 459 sheet: 0.33 (0.20), residues: 713 loop : -2.47 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 400 HIS 0.004 0.001 HIS B 148 PHE 0.021 0.002 PHE F 37 TYR 0.010 0.001 TYR l 36 ARG 0.005 0.000 ARG B 420 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 312 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 LYS cc_start: 0.6554 (tttt) cc_final: 0.5892 (tttp) REVERT: D 25 TYR cc_start: 0.6095 (OUTLIER) cc_final: 0.4868 (p90) REVERT: B 27 HIS cc_start: 0.8034 (OUTLIER) cc_final: 0.7290 (t-90) REVERT: B 136 GLU cc_start: 0.6386 (tt0) cc_final: 0.6129 (tt0) REVERT: B 168 GLU cc_start: 0.6371 (mt-10) cc_final: 0.6059 (mt-10) REVERT: C 175 ARG cc_start: 0.5553 (ptt-90) cc_final: 0.5159 (ptp90) outliers start: 89 outliers final: 78 residues processed: 365 average time/residue: 0.2603 time to fit residues: 148.6086 Evaluate side-chains 382 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 302 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 172 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 177 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 151 optimal weight: 50.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.185473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.123954 restraints weight = 20151.192| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.25 r_work: 0.3241 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17196 Z= 0.235 Angle : 0.693 14.632 23304 Z= 0.349 Chirality : 0.047 0.748 2641 Planarity : 0.004 0.047 2942 Dihedral : 7.065 71.583 2514 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.44 % Favored : 89.37 % Rotamer: Outliers : 4.67 % Allowed : 22.40 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.31 (0.18), residues: 2174 helix: 0.46 (0.25), residues: 459 sheet: 0.55 (0.21), residues: 629 loop : -2.46 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 400 HIS 0.004 0.001 HIS B 148 PHE 0.022 0.002 PHE F 37 TYR 0.010 0.001 TYR A 332 ARG 0.005 0.000 ARG B 420 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3903.38 seconds wall clock time: 72 minutes 8.46 seconds (4328.46 seconds total)