Starting phenix.real_space_refine on Wed Feb 14 23:45:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2q_26318/02_2024/7u2q_26318.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2q_26318/02_2024/7u2q_26318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2q_26318/02_2024/7u2q_26318.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2q_26318/02_2024/7u2q_26318.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2q_26318/02_2024/7u2q_26318.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2q_26318/02_2024/7u2q_26318.pdb" } resolution = 3.2 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= 0.008 sd= 0.143 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 6656 2.51 5 N 1780 2.21 5 O 2016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "B PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 398": "OE1" <-> "OE2" Residue "C PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "D PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 398": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10536 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2606 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 320} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2606 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 320} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2606 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 320} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2606 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 320} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.86, per 1000 atoms: 0.56 Number of scatterers: 10536 At special positions: 0 Unit cell: (119.48, 119.48, 64.96, 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 84 16.00 O 2016 8.00 N 1780 7.00 C 6656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.02 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.07 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 231 " distance=2.02 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 238 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 290 " distance=2.02 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 335 " distance=2.04 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 446 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.02 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.07 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 231 " distance=2.02 Simple disulfide: pdb=" SG CYS B 233 " - pdb=" SG CYS B 238 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 290 " distance=2.02 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 335 " distance=2.04 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 446 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.02 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.07 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 231 " distance=2.02 Simple disulfide: pdb=" SG CYS C 233 " - pdb=" SG CYS C 238 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 290 " distance=2.02 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 335 " distance=2.04 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 446 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.02 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.07 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 231 " distance=2.02 Simple disulfide: pdb=" SG CYS D 233 " - pdb=" SG CYS D 238 " distance=2.03 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 290 " distance=2.02 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 335 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 446 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 88 " " NAG A 502 " - " ASN A 235 " " NAG B 501 " - " ASN B 88 " " NAG B 502 " - " ASN B 235 " " NAG C 501 " - " ASN C 88 " " NAG C 502 " - " ASN C 235 " " NAG D 501 " - " ASN D 88 " " NAG D 502 " - " ASN D 235 " Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 1.7 seconds 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 24 sheets defined 3.3% alpha, 43.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.893A pdb=" N LYS A 111 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.893A pdb=" N LYS B 111 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.893A pdb=" N LYS C 111 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 414 Processing helix chain 'D' and resid 107 through 111 removed outlier: 3.893A pdb=" N LYS D 111 " --> pdb=" O ILE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 103 removed outlier: 6.752A pdb=" N SER A 444 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS A 102 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER A 442 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR A 402 " --> pdb=" O GLU A 425 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 389 " --> pdb=" O TRP A 375 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE A 371 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLY A 395 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN A 369 " --> pdb=" O GLY A 395 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124 removed outlier: 6.791A pdb=" N LEU A 158 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 185 removed outlier: 3.516A pdb=" N SER A 180 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 204 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR A 215 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU A 206 " --> pdb=" O THR A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 225 removed outlier: 3.645A pdb=" N ALA A 232 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 removed outlier: 7.129A pdb=" N TYR A 253 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU A 268 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 255 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER A 266 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ARG A 257 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 277 through 284 removed outlier: 4.891A pdb=" N CYS A 279 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL A 291 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS A 281 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR A 289 " --> pdb=" O CYS A 281 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLU A 287 " --> pdb=" O PRO A 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 103 removed outlier: 6.752A pdb=" N SER B 444 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS B 102 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER B 442 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR B 402 " --> pdb=" O GLU B 425 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 389 " --> pdb=" O TRP B 375 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE B 371 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLY B 395 " --> pdb=" O ASN B 369 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN B 369 " --> pdb=" O GLY B 395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 121 through 124 removed outlier: 6.791A pdb=" N LEU B 158 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 180 through 185 removed outlier: 3.516A pdb=" N SER B 180 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA B 204 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR B 215 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU B 206 " --> pdb=" O THR B 213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 224 through 225 removed outlier: 3.645A pdb=" N ALA B 232 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 224 through 225 removed outlier: 7.129A pdb=" N TYR B 253 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU B 268 " --> pdb=" O TYR B 253 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 255 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER B 266 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ARG B 257 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 277 through 284 removed outlier: 4.891A pdb=" N CYS B 279 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL B 291 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS B 281 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR B 289 " --> pdb=" O CYS B 281 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLU B 287 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 103 removed outlier: 6.752A pdb=" N SER C 444 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS C 102 " --> pdb=" O SER C 442 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER C 442 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR C 402 " --> pdb=" O GLU C 425 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE C 389 " --> pdb=" O TRP C 375 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE C 371 " --> pdb=" O ILE C 393 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLY C 395 " --> pdb=" O ASN C 369 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN C 369 " --> pdb=" O GLY C 395 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 121 through 124 removed outlier: 6.791A pdb=" N LEU C 158 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 180 through 185 removed outlier: 3.516A pdb=" N SER C 180 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA C 204 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR C 215 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU C 206 " --> pdb=" O THR C 213 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 224 through 225 removed outlier: 3.645A pdb=" N ALA C 232 " --> pdb=" O PHE C 239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 224 through 225 removed outlier: 7.129A pdb=" N TYR C 253 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU C 268 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE C 255 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER C 266 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ARG C 257 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 277 through 284 removed outlier: 4.891A pdb=" N CYS C 279 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL C 291 " --> pdb=" O CYS C 279 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS C 281 " --> pdb=" O THR C 289 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR C 289 " --> pdb=" O CYS C 281 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLU C 287 " --> pdb=" O PRO C 283 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 96 through 103 removed outlier: 6.752A pdb=" N SER D 444 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS D 102 " --> pdb=" O SER D 442 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER D 442 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR D 402 " --> pdb=" O GLU D 425 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE D 389 " --> pdb=" O TRP D 375 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE D 371 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLY D 395 " --> pdb=" O ASN D 369 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN D 369 " --> pdb=" O GLY D 395 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 121 through 124 removed outlier: 6.791A pdb=" N LEU D 158 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 180 through 185 removed outlier: 3.516A pdb=" N SER D 180 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA D 204 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR D 215 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU D 206 " --> pdb=" O THR D 213 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 224 through 225 removed outlier: 3.645A pdb=" N ALA D 232 " --> pdb=" O PHE D 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 224 through 225 removed outlier: 7.129A pdb=" N TYR D 253 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU D 268 " --> pdb=" O TYR D 253 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE D 255 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER D 266 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ARG D 257 " --> pdb=" O VAL D 264 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 277 through 284 removed outlier: 4.891A pdb=" N CYS D 279 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL D 291 " --> pdb=" O CYS D 279 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS D 281 " --> pdb=" O THR D 289 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR D 289 " --> pdb=" O CYS D 281 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU D 287 " --> pdb=" O PRO D 283 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 936 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: 3.32 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2658 1.33 - 1.46: 3154 1.46 - 1.60: 4892 1.60 - 1.73: 0 1.73 - 1.86: 104 Bond restraints: 10808 Sorted by residual: bond pdb=" N GLU C 119 " pdb=" CA GLU C 119 " ideal model delta sigma weight residual 1.458 1.497 -0.040 7.40e-03 1.83e+04 2.87e+01 bond pdb=" N GLU B 119 " pdb=" CA GLU B 119 " ideal model delta sigma weight residual 1.458 1.497 -0.040 7.40e-03 1.83e+04 2.87e+01 bond pdb=" N GLU A 119 " pdb=" CA GLU A 119 " ideal model delta sigma weight residual 1.458 1.497 -0.040 7.40e-03 1.83e+04 2.87e+01 bond pdb=" N GLU D 119 " pdb=" CA GLU D 119 " ideal model delta sigma weight residual 1.458 1.497 -0.040 7.40e-03 1.83e+04 2.87e+01 bond pdb=" N VAL D 106 " pdb=" CA VAL D 106 " ideal model delta sigma weight residual 1.452 1.496 -0.044 1.18e-02 7.18e+03 1.37e+01 ... (remaining 10803 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.76: 420 106.76 - 113.67: 5604 113.67 - 120.59: 4754 120.59 - 127.50: 3742 127.50 - 134.42: 156 Bond angle restraints: 14676 Sorted by residual: angle pdb=" C GLY B 197 " pdb=" N PRO B 198 " pdb=" CA PRO B 198 " ideal model delta sigma weight residual 119.85 127.52 -7.67 1.01e+00 9.80e-01 5.77e+01 angle pdb=" C GLY C 197 " pdb=" N PRO C 198 " pdb=" CA PRO C 198 " ideal model delta sigma weight residual 119.85 127.52 -7.67 1.01e+00 9.80e-01 5.77e+01 angle pdb=" C GLY A 197 " pdb=" N PRO A 198 " pdb=" CA PRO A 198 " ideal model delta sigma weight residual 119.85 127.52 -7.67 1.01e+00 9.80e-01 5.77e+01 angle pdb=" C GLY D 197 " pdb=" N PRO D 198 " pdb=" CA PRO D 198 " ideal model delta sigma weight residual 119.85 127.52 -7.67 1.01e+00 9.80e-01 5.77e+01 angle pdb=" C ASP D 376 " pdb=" N PRO D 377 " pdb=" CA PRO D 377 " ideal model delta sigma weight residual 119.56 126.55 -6.99 1.01e+00 9.80e-01 4.79e+01 ... (remaining 14671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 5995 16.01 - 32.02: 321 32.02 - 48.03: 84 48.03 - 64.05: 48 64.05 - 80.06: 8 Dihedral angle restraints: 6456 sinusoidal: 2640 harmonic: 3816 Sorted by residual: dihedral pdb=" CB CYS B 318 " pdb=" SG CYS B 318 " pdb=" SG CYS B 335 " pdb=" CB CYS B 335 " ideal model delta sinusoidal sigma weight residual 93.00 119.03 -26.03 1 1.00e+01 1.00e-02 9.74e+00 dihedral pdb=" CB CYS A 318 " pdb=" SG CYS A 318 " pdb=" SG CYS A 335 " pdb=" CB CYS A 335 " ideal model delta sinusoidal sigma weight residual 93.00 119.03 -26.03 1 1.00e+01 1.00e-02 9.74e+00 dihedral pdb=" CB CYS C 318 " pdb=" SG CYS C 318 " pdb=" SG CYS C 335 " pdb=" CB CYS C 335 " ideal model delta sinusoidal sigma weight residual 93.00 119.03 -26.03 1 1.00e+01 1.00e-02 9.74e+00 ... (remaining 6453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 925 0.068 - 0.135: 456 0.135 - 0.203: 137 0.203 - 0.270: 54 0.270 - 0.338: 16 Chirality restraints: 1588 Sorted by residual: chirality pdb=" CB VAL D 83 " pdb=" CA VAL D 83 " pdb=" CG1 VAL D 83 " pdb=" CG2 VAL D 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.97 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CB VAL C 83 " pdb=" CA VAL C 83 " pdb=" CG1 VAL C 83 " pdb=" CG2 VAL C 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.97 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CB VAL A 83 " pdb=" CA VAL A 83 " pdb=" CG1 VAL A 83 " pdb=" CG2 VAL A 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.97 0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 1585 not shown) Planarity restraints: 1876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 502 " -0.046 2.00e-02 2.50e+03 3.79e-02 1.80e+01 pdb=" C7 NAG A 502 " 0.013 2.00e-02 2.50e+03 pdb=" C8 NAG A 502 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG A 502 " 0.060 2.00e-02 2.50e+03 pdb=" O7 NAG A 502 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 502 " -0.046 2.00e-02 2.50e+03 3.79e-02 1.80e+01 pdb=" C7 NAG B 502 " 0.013 2.00e-02 2.50e+03 pdb=" C8 NAG B 502 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG B 502 " 0.060 2.00e-02 2.50e+03 pdb=" O7 NAG B 502 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 502 " -0.046 2.00e-02 2.50e+03 3.79e-02 1.80e+01 pdb=" C7 NAG C 502 " 0.013 2.00e-02 2.50e+03 pdb=" C8 NAG C 502 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG C 502 " 0.060 2.00e-02 2.50e+03 pdb=" O7 NAG C 502 " 0.008 2.00e-02 2.50e+03 ... (remaining 1873 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 5584 3.00 - 3.47: 9443 3.47 - 3.95: 17936 3.95 - 4.42: 21194 4.42 - 4.90: 34347 Nonbonded interactions: 88504 Sorted by model distance: nonbonded pdb=" N ASP B 416 " pdb=" OD1 ASP B 416 " model vdw 2.525 2.520 nonbonded pdb=" N ASP A 416 " pdb=" OD1 ASP A 416 " model vdw 2.525 2.520 nonbonded pdb=" N ASP D 416 " pdb=" OD1 ASP D 416 " model vdw 2.525 2.520 nonbonded pdb=" N ASP C 416 " pdb=" OD1 ASP C 416 " model vdw 2.525 2.520 nonbonded pdb=" N SER D 125 " pdb=" O SER D 125 " model vdw 2.534 2.496 ... (remaining 88499 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.370 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 30.060 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 0.013 0.072 10808 Z= 0.901 Angle : 1.519 7.674 14676 Z= 1.075 Chirality : 0.094 0.338 1588 Planarity : 0.006 0.038 1868 Dihedral : 12.140 80.057 3920 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.96 % Favored : 95.73 % Rotamer: Outliers : 4.83 % Allowed : 2.76 % Favored : 92.41 % 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: -0.35 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: 0.19 (0.24), residues: 456 loop : -0.44 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 179 HIS 0.003 0.001 HIS D 275 PHE 0.019 0.004 PHE B 406 TYR 0.038 0.007 TYR D 276 ARG 0.003 0.001 ARG C 225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 308 time to evaluate : 1.207 Fit side-chains REVERT: A 159 MET cc_start: 0.8596 (mtp) cc_final: 0.8376 (mtt) REVERT: A 226 THR cc_start: 0.9115 (t) cc_final: 0.8903 (t) REVERT: B 159 MET cc_start: 0.8597 (mtp) cc_final: 0.8377 (mtt) REVERT: B 226 THR cc_start: 0.9108 (t) cc_final: 0.8895 (t) REVERT: C 159 MET cc_start: 0.8589 (mtp) cc_final: 0.8372 (mtt) REVERT: C 226 THR cc_start: 0.9116 (t) cc_final: 0.8903 (t) REVERT: D 159 MET cc_start: 0.8587 (mtp) cc_final: 0.8371 (mtt) REVERT: D 226 THR cc_start: 0.9113 (t) cc_final: 0.8896 (t) outliers start: 56 outliers final: 0 residues processed: 348 average time/residue: 0.2456 time to fit residues: 119.0696 Evaluate side-chains 140 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 227 GLN A 369 ASN B 136 GLN B 189 ASN B 227 GLN B 369 ASN C 136 GLN C 227 GLN C 369 ASN D 136 GLN D 227 GLN D 369 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10808 Z= 0.195 Angle : 0.566 5.073 14676 Z= 0.311 Chirality : 0.048 0.133 1588 Planarity : 0.005 0.039 1868 Dihedral : 4.887 15.934 1600 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.22 % Favored : 98.48 % Rotamer: Outliers : 1.98 % Allowed : 8.79 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: 0.38 (0.20), residues: 508 loop : -0.07 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 179 HIS 0.003 0.001 HIS C 185 PHE 0.021 0.002 PHE D 406 TYR 0.007 0.001 TYR B 253 ARG 0.005 0.001 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 181 time to evaluate : 1.206 Fit side-chains REVERT: A 226 THR cc_start: 0.9111 (t) cc_final: 0.8908 (t) REVERT: A 258 ILE cc_start: 0.8884 (mt) cc_final: 0.8674 (mt) REVERT: A 314 ILE cc_start: 0.8402 (pt) cc_final: 0.8073 (mt) REVERT: B 189 ASN cc_start: 0.8687 (m110) cc_final: 0.8408 (m110) REVERT: B 226 THR cc_start: 0.9104 (t) cc_final: 0.8901 (t) REVERT: B 258 ILE cc_start: 0.8890 (mt) cc_final: 0.8675 (mt) REVERT: B 314 ILE cc_start: 0.8422 (pt) cc_final: 0.8095 (mt) REVERT: C 226 THR cc_start: 0.9112 (t) cc_final: 0.8907 (t) REVERT: C 258 ILE cc_start: 0.8888 (mt) cc_final: 0.8681 (mt) REVERT: C 314 ILE cc_start: 0.8411 (pt) cc_final: 0.8088 (mt) REVERT: D 226 THR cc_start: 0.9104 (t) cc_final: 0.8898 (t) REVERT: D 258 ILE cc_start: 0.8889 (mt) cc_final: 0.8682 (mt) REVERT: D 314 ILE cc_start: 0.8406 (pt) cc_final: 0.8084 (mt) outliers start: 23 outliers final: 11 residues processed: 197 average time/residue: 0.2110 time to fit residues: 60.6312 Evaluate side-chains 175 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 164 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 396 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 222 ASN C 222 ASN D 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 10808 Z= 0.379 Angle : 0.584 5.318 14676 Z= 0.315 Chirality : 0.050 0.140 1588 Planarity : 0.005 0.043 1868 Dihedral : 4.697 16.145 1600 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.97 % Favored : 96.72 % Rotamer: Outliers : 2.07 % Allowed : 11.38 % Favored : 86.55 % 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: -0.13 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: 0.29 (0.20), residues: 552 loop : -0.30 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 179 HIS 0.005 0.002 HIS C 185 PHE 0.022 0.003 PHE D 406 TYR 0.009 0.002 TYR C 316 ARG 0.006 0.001 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 1.202 Fit side-chains REVERT: A 89 SER cc_start: 0.9094 (p) cc_final: 0.8874 (t) REVERT: A 226 THR cc_start: 0.9265 (t) cc_final: 0.9038 (t) REVERT: B 89 SER cc_start: 0.9091 (p) cc_final: 0.8880 (t) REVERT: B 189 ASN cc_start: 0.8865 (m110) cc_final: 0.8485 (m-40) REVERT: B 200 ASN cc_start: 0.8062 (t0) cc_final: 0.7740 (t0) REVERT: B 226 THR cc_start: 0.9258 (t) cc_final: 0.9036 (t) REVERT: B 314 ILE cc_start: 0.8412 (pt) cc_final: 0.8063 (mt) REVERT: C 89 SER cc_start: 0.9061 (p) cc_final: 0.8837 (t) REVERT: C 200 ASN cc_start: 0.7992 (t0) cc_final: 0.7780 (t0) REVERT: C 226 THR cc_start: 0.9268 (t) cc_final: 0.9031 (t) REVERT: C 314 ILE cc_start: 0.8414 (pt) cc_final: 0.8072 (mt) REVERT: D 89 SER cc_start: 0.9096 (p) cc_final: 0.8881 (t) REVERT: D 200 ASN cc_start: 0.7999 (t0) cc_final: 0.7762 (t0) REVERT: D 226 THR cc_start: 0.9257 (t) cc_final: 0.9017 (t) REVERT: D 314 ILE cc_start: 0.8420 (pt) cc_final: 0.8062 (mt) outliers start: 24 outliers final: 23 residues processed: 175 average time/residue: 0.2494 time to fit residues: 60.3095 Evaluate side-chains 164 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 396 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10808 Z= 0.173 Angle : 0.480 4.487 14676 Z= 0.260 Chirality : 0.047 0.134 1588 Planarity : 0.004 0.040 1868 Dihedral : 4.268 15.826 1600 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.75 % Favored : 97.94 % Rotamer: Outliers : 2.59 % Allowed : 11.47 % Favored : 85.95 % 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: -0.26 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: 0.15 (0.20), residues: 552 loop : -0.35 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 179 HIS 0.005 0.001 HIS A 185 PHE 0.015 0.002 PHE C 406 TYR 0.008 0.001 TYR A 316 ARG 0.003 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 154 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.9102 (p) cc_final: 0.8895 (t) REVERT: A 170 TYR cc_start: 0.8679 (m-80) cc_final: 0.8449 (m-10) REVERT: A 311 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7006 (mt-10) REVERT: B 89 SER cc_start: 0.9099 (p) cc_final: 0.8898 (t) REVERT: B 170 TYR cc_start: 0.8670 (m-80) cc_final: 0.8441 (m-10) REVERT: B 189 ASN cc_start: 0.8901 (m110) cc_final: 0.8511 (m-40) REVERT: B 200 ASN cc_start: 0.8058 (t0) cc_final: 0.7695 (t0) REVERT: B 311 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7024 (mt-10) REVERT: C 89 SER cc_start: 0.9068 (p) cc_final: 0.8854 (t) REVERT: C 170 TYR cc_start: 0.8672 (m-80) cc_final: 0.8443 (m-10) REVERT: C 200 ASN cc_start: 0.8017 (t0) cc_final: 0.7773 (t0) REVERT: C 311 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7028 (mt-10) REVERT: D 89 SER cc_start: 0.9104 (p) cc_final: 0.8901 (t) REVERT: D 170 TYR cc_start: 0.8685 (m-80) cc_final: 0.8452 (m-10) REVERT: D 200 ASN cc_start: 0.8026 (t0) cc_final: 0.7753 (t0) REVERT: D 311 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7039 (mt-10) outliers start: 30 outliers final: 26 residues processed: 178 average time/residue: 0.2221 time to fit residues: 56.2339 Evaluate side-chains 165 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 135 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 396 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 0 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10808 Z= 0.199 Angle : 0.489 5.423 14676 Z= 0.262 Chirality : 0.047 0.140 1588 Planarity : 0.004 0.042 1868 Dihedral : 4.159 16.121 1600 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.75 % Favored : 97.94 % Rotamer: Outliers : 2.93 % Allowed : 12.67 % Favored : 84.40 % 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: -0.16 (0.22), residues: 1312 helix: None (None), residues: 0 sheet: 0.18 (0.20), residues: 580 loop : -0.27 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 179 HIS 0.004 0.001 HIS B 185 PHE 0.017 0.002 PHE D 406 TYR 0.008 0.001 TYR B 276 ARG 0.003 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 145 time to evaluate : 1.103 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 170 TYR cc_start: 0.8698 (m-80) cc_final: 0.8496 (m-10) REVERT: A 311 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7019 (mt-10) REVERT: B 170 TYR cc_start: 0.8689 (m-80) cc_final: 0.8488 (m-10) REVERT: B 189 ASN cc_start: 0.8912 (m110) cc_final: 0.8502 (m-40) REVERT: B 311 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7042 (mt-10) REVERT: C 311 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7058 (mt-10) REVERT: D 170 TYR cc_start: 0.8704 (m-80) cc_final: 0.8502 (m-10) REVERT: D 311 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7029 (mt-10) outliers start: 34 outliers final: 30 residues processed: 173 average time/residue: 0.2220 time to fit residues: 54.5182 Evaluate side-chains 164 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 396 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 10.0000 chunk 25 optimal weight: 0.0870 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 106 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN C 136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10808 Z= 0.134 Angle : 0.461 5.579 14676 Z= 0.248 Chirality : 0.047 0.134 1588 Planarity : 0.004 0.040 1868 Dihedral : 3.947 16.386 1600 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.52 % Favored : 98.17 % Rotamer: Outliers : 3.02 % Allowed : 13.19 % Favored : 83.79 % 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: 0.01 (0.22), residues: 1312 helix: None (None), residues: 0 sheet: 0.20 (0.21), residues: 576 loop : -0.05 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 179 HIS 0.004 0.001 HIS A 185 PHE 0.012 0.002 PHE B 406 TYR 0.012 0.001 TYR A 274 ARG 0.004 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 1.260 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 311 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6978 (mt-10) REVERT: B 170 TYR cc_start: 0.8696 (m-80) cc_final: 0.8495 (m-10) REVERT: B 189 ASN cc_start: 0.8853 (m110) cc_final: 0.8498 (m-40) REVERT: B 311 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6993 (mt-10) REVERT: C 311 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7005 (mt-10) REVERT: D 311 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7005 (mt-10) outliers start: 35 outliers final: 21 residues processed: 169 average time/residue: 0.2583 time to fit residues: 61.0245 Evaluate side-chains 152 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 362 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 127 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 10808 Z= 0.411 Angle : 0.582 6.049 14676 Z= 0.311 Chirality : 0.050 0.144 1588 Planarity : 0.005 0.044 1868 Dihedral : 4.468 16.100 1600 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.20 % Favored : 96.49 % Rotamer: Outliers : 4.31 % Allowed : 12.84 % Favored : 82.84 % 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: -0.55 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: -0.11 (0.20), residues: 576 loop : -0.50 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 179 HIS 0.005 0.002 HIS D 185 PHE 0.024 0.003 PHE D 406 TYR 0.011 0.002 TYR A 316 ARG 0.009 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 133 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 35 residues processed: 173 average time/residue: 0.2248 time to fit residues: 55.5215 Evaluate side-chains 152 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 117 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 363 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 86 optimal weight: 0.0370 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 100 optimal weight: 0.0970 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10808 Z= 0.154 Angle : 0.482 7.128 14676 Z= 0.262 Chirality : 0.047 0.132 1588 Planarity : 0.004 0.041 1868 Dihedral : 4.072 16.680 1600 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.60 % Favored : 98.09 % Rotamer: Outliers : 2.24 % Allowed : 15.17 % Favored : 82.59 % 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: -0.34 (0.22), residues: 1312 helix: None (None), residues: 0 sheet: -0.13 (0.20), residues: 576 loop : -0.19 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 179 HIS 0.002 0.001 HIS B 185 PHE 0.017 0.002 PHE B 406 TYR 0.011 0.001 TYR D 274 ARG 0.006 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 24 residues processed: 151 average time/residue: 0.2389 time to fit residues: 50.9365 Evaluate side-chains 147 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 362 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.2980 chunk 121 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 10808 Z= 0.208 Angle : 0.508 14.416 14676 Z= 0.273 Chirality : 0.048 0.298 1588 Planarity : 0.004 0.041 1868 Dihedral : 4.062 16.932 1600 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.83 % Favored : 97.87 % Rotamer: Outliers : 2.67 % Allowed : 15.17 % Favored : 82.16 % 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: -0.35 (0.22), residues: 1312 helix: None (None), residues: 0 sheet: -0.15 (0.20), residues: 576 loop : -0.20 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 296 HIS 0.002 0.001 HIS D 185 PHE 0.019 0.002 PHE C 406 TYR 0.010 0.001 TYR A 274 ARG 0.006 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 30 residues processed: 148 average time/residue: 0.2249 time to fit residues: 47.6309 Evaluate side-chains 152 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 389 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 10808 Z= 0.225 Angle : 0.527 15.930 14676 Z= 0.282 Chirality : 0.048 0.236 1588 Planarity : 0.004 0.041 1868 Dihedral : 4.083 17.927 1600 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.68 % Favored : 98.02 % Rotamer: Outliers : 2.67 % Allowed : 15.17 % Favored : 82.16 % 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: -0.34 (0.22), residues: 1312 helix: None (None), residues: 0 sheet: -0.13 (0.20), residues: 568 loop : -0.20 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 179 HIS 0.002 0.001 HIS C 185 PHE 0.019 0.002 PHE C 406 TYR 0.011 0.001 TYR C 274 ARG 0.006 0.000 ARG D 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 31 residues processed: 148 average time/residue: 0.2244 time to fit residues: 47.3976 Evaluate side-chains 154 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 123 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 389 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.0970 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.145287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.112282 restraints weight = 12422.268| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.63 r_work: 0.3201 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 10808 Z= 0.163 Angle : 0.493 15.514 14676 Z= 0.264 Chirality : 0.047 0.210 1588 Planarity : 0.004 0.039 1868 Dihedral : 3.930 17.103 1600 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.83 % Favored : 97.87 % Rotamer: Outliers : 2.67 % Allowed : 15.43 % Favored : 81.90 % 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: -0.22 (0.22), residues: 1312 helix: None (None), residues: 0 sheet: -0.09 (0.20), residues: 568 loop : -0.07 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 179 HIS 0.002 0.001 HIS D 185 PHE 0.016 0.002 PHE C 406 TYR 0.011 0.001 TYR A 274 ARG 0.006 0.000 ARG A 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2364.00 seconds wall clock time: 43 minutes 32.81 seconds (2612.81 seconds total)