Starting phenix.real_space_refine on Tue Aug 6 04:43:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvi_41643/08_2024/8tvi_41643.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvi_41643/08_2024/8tvi_41643.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/8tvi_41643/08_2024/8tvi_41643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvi_41643/08_2024/8tvi_41643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvi_41643/08_2024/8tvi_41643.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvi_41643/08_2024/8tvi_41643.cif" } 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= 0.000 sd= 0.083 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 96 5.16 5 C 9832 2.51 5 N 2540 2.21 5 O 2852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 592": "NH1" <-> "NH2" Residue "A PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 463": "NH1" <-> "NH2" Residue "C TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 592": "NH1" <-> "NH2" Residue "C PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 239": "NH1" <-> "NH2" Residue "D PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 463": "NH1" <-> "NH2" Residue "D TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 466": "NH1" <-> "NH2" Residue "D TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 592": "NH1" <-> "NH2" Residue "D PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15324 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3816 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 486} Chain breaks: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 109 Chain: "B" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3816 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 486} Chain breaks: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 109 Chain: "C" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3816 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 486} Chain breaks: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 109 Chain: "D" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3816 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 486} Chain breaks: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 109 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.35, per 1000 atoms: 0.61 Number of scatterers: 15324 At special positions: 0 Unit cell: (143.29, 143.29, 123.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 96 16.00 O 2852 8.00 N 2540 7.00 C 9832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 604 " distance=2.04 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 243 " distance=2.01 Simple disulfide: pdb=" SG CYS A 285 " - pdb=" SG CYS A 298 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 396 " distance=2.08 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 502 " distance=2.03 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 577 " distance=2.02 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS B 219 " - pdb=" SG CYS B 243 " distance=2.01 Simple disulfide: pdb=" SG CYS B 285 " - pdb=" SG CYS B 298 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 396 " distance=2.08 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 502 " distance=2.03 Simple disulfide: pdb=" SG CYS B 494 " - pdb=" SG CYS B 506 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 577 " distance=2.02 Simple disulfide: pdb=" SG CYS C 188 " - pdb=" SG CYS C 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 219 " - pdb=" SG CYS C 243 " distance=2.01 Simple disulfide: pdb=" SG CYS C 285 " - pdb=" SG CYS C 298 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 396 " distance=2.08 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 502 " distance=2.03 Simple disulfide: pdb=" SG CYS C 494 " - pdb=" SG CYS C 506 " distance=2.03 Simple disulfide: pdb=" SG CYS C 568 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS D 188 " - pdb=" SG CYS D 604 " distance=2.04 Simple disulfide: pdb=" SG CYS D 219 " - pdb=" SG CYS D 243 " distance=2.01 Simple disulfide: pdb=" SG CYS D 285 " - pdb=" SG CYS D 298 " distance=2.04 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 396 " distance=2.08 Simple disulfide: pdb=" SG CYS D 384 " - pdb=" SG CYS D 502 " distance=2.03 Simple disulfide: pdb=" SG CYS D 494 " - pdb=" SG CYS D 506 " distance=2.03 Simple disulfide: pdb=" SG CYS D 568 " - pdb=" SG CYS D 577 " distance=2.02 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 701 " - " ASN A 189 " " NAG B 701 " - " ASN B 189 " " NAG C 701 " - " ASN C 189 " " NAG D 701 " - " ASN D 189 " Time building additional restraints: 5.62 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" ND1 HIS A 548 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 194 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" ND1 HIS B 548 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 194 " pdb=" ZN C 702 " pdb="ZN ZN C 702 " - pdb=" ND1 HIS C 548 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 194 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" ND1 HIS D 548 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 194 " 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3832 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 24 sheets defined 19.3% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 68 through 86 Processing helix chain 'A' and resid 86 through 99 removed outlier: 3.514A pdb=" N VAL A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.936A pdb=" N LYS A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 141 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 391 through 400 removed outlier: 3.938A pdb=" N VAL A 400 " --> pdb=" O CYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'B' and resid 69 through 86 Processing helix chain 'B' and resid 86 through 99 removed outlier: 3.514A pdb=" N VAL B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.936A pdb=" N LYS B 103 " --> pdb=" O GLU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 141 Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 391 through 400 removed outlier: 3.938A pdb=" N VAL B 400 " --> pdb=" O CYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 423 Processing helix chain 'B' and resid 433 through 437 Processing helix chain 'C' and resid 69 through 86 Processing helix chain 'C' and resid 86 through 99 removed outlier: 3.514A pdb=" N VAL C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 113 removed outlier: 3.936A pdb=" N LYS C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 141 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 391 through 400 removed outlier: 3.938A pdb=" N VAL C 400 " --> pdb=" O CYS C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 423 Processing helix chain 'C' and resid 433 through 437 Processing helix chain 'D' and resid 69 through 86 Processing helix chain 'D' and resid 86 through 99 removed outlier: 3.514A pdb=" N VAL D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 113 removed outlier: 3.936A pdb=" N LYS D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 141 Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 391 through 400 removed outlier: 3.938A pdb=" N VAL D 400 " --> pdb=" O CYS D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 423 Processing helix chain 'D' and resid 433 through 437 Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 177 through 178 current: chain 'A' and resid 574 through 584 removed outlier: 4.582A pdb=" N ILE A 575 " --> pdb=" O VAL A 600 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 227 removed outlier: 5.442A pdb=" N TYR A 220 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG A 239 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASN A 222 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU A 237 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 250 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS A 240 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE A 248 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE A 251 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER A 275 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE A 253 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL A 273 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU A 255 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 289 removed outlier: 6.848A pdb=" N SER A 299 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N CYS A 285 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU A 297 " --> pdb=" O CYS A 285 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL A 287 " --> pdb=" O TRP A 295 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP A 295 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 338 through 339 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 338 through 339 current: chain 'A' and resid 360 through 370 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 360 through 370 current: chain 'A' and resid 405 through 418 Processing sheet with id=AA5, first strand: chain 'A' and resid 443 through 448 Processing sheet with id=AA6, first strand: chain 'A' and resid 514 through 516 removed outlier: 4.512A pdb=" N SER A 538 " --> pdb=" O ILE A 554 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 177 through 178 current: chain 'B' and resid 574 through 584 removed outlier: 4.582A pdb=" N ILE B 575 " --> pdb=" O VAL B 600 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 218 through 227 removed outlier: 5.442A pdb=" N TYR B 220 " --> pdb=" O ARG B 239 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG B 239 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASN B 222 " --> pdb=" O GLU B 237 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU B 237 " --> pdb=" O ASN B 222 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 250 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS B 240 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE B 248 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE B 251 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER B 275 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE B 253 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL B 273 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU B 255 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 282 through 289 removed outlier: 6.848A pdb=" N SER B 299 " --> pdb=" O ASN B 283 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N CYS B 285 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B 297 " --> pdb=" O CYS B 285 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL B 287 " --> pdb=" O TRP B 295 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP B 295 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 338 through 339 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 338 through 339 current: chain 'B' and resid 360 through 370 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 360 through 370 current: chain 'B' and resid 405 through 418 Processing sheet with id=AB2, first strand: chain 'B' and resid 443 through 448 Processing sheet with id=AB3, first strand: chain 'B' and resid 514 through 516 removed outlier: 4.512A pdb=" N SER B 538 " --> pdb=" O ILE B 554 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 177 through 178 current: chain 'C' and resid 574 through 584 removed outlier: 4.582A pdb=" N ILE C 575 " --> pdb=" O VAL C 600 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 218 through 227 removed outlier: 5.442A pdb=" N TYR C 220 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG C 239 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASN C 222 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU C 237 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 250 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS C 240 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE C 248 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE C 251 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER C 275 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE C 253 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL C 273 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU C 255 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 282 through 289 removed outlier: 6.848A pdb=" N SER C 299 " --> pdb=" O ASN C 283 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N CYS C 285 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU C 297 " --> pdb=" O CYS C 285 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL C 287 " --> pdb=" O TRP C 295 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP C 295 " --> pdb=" O VAL C 287 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 338 through 339 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 338 through 339 current: chain 'C' and resid 360 through 370 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 360 through 370 current: chain 'C' and resid 405 through 418 Processing sheet with id=AB8, first strand: chain 'C' and resid 443 through 448 Processing sheet with id=AB9, first strand: chain 'C' and resid 514 through 516 removed outlier: 4.512A pdb=" N SER C 538 " --> pdb=" O ILE C 554 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 177 through 178 current: chain 'D' and resid 574 through 584 removed outlier: 4.582A pdb=" N ILE D 575 " --> pdb=" O VAL D 600 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 218 through 227 removed outlier: 5.442A pdb=" N TYR D 220 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG D 239 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASN D 222 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU D 237 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER D 250 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS D 240 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE D 248 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE D 251 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER D 275 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE D 253 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL D 273 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU D 255 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 282 through 289 removed outlier: 6.848A pdb=" N SER D 299 " --> pdb=" O ASN D 283 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N CYS D 285 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU D 297 " --> pdb=" O CYS D 285 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL D 287 " --> pdb=" O TRP D 295 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP D 295 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 338 through 339 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 338 through 339 current: chain 'D' and resid 360 through 370 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 360 through 370 current: chain 'D' and resid 405 through 418 Processing sheet with id=AC5, first strand: chain 'D' and resid 443 through 448 Processing sheet with id=AC6, first strand: chain 'D' and resid 514 through 516 removed outlier: 4.512A pdb=" N SER D 538 " --> pdb=" O ILE D 554 " (cutoff:3.500A) 553 hydrogen bonds defined for protein. 1503 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: 4.82 Time building geometry restraints manager: 6.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2740 1.32 - 1.45: 3940 1.45 - 1.57: 8832 1.57 - 1.70: 8 1.70 - 1.82: 136 Bond restraints: 15656 Sorted by residual: bond pdb=" C LYS D 103 " pdb=" O LYS D 103 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" C LYS B 103 " pdb=" O LYS B 103 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" C LYS A 103 " pdb=" O LYS A 103 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" C LYS C 103 " pdb=" O LYS C 103 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" C5 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.413 1.478 -0.065 2.00e-02 2.50e+03 1.07e+01 ... (remaining 15651 not shown) Histogram of bond angle deviations from ideal: 98.20 - 105.31: 448 105.31 - 112.41: 7812 112.41 - 119.52: 4676 119.52 - 126.63: 8252 126.63 - 133.73: 148 Bond angle restraints: 21336 Sorted by residual: angle pdb=" C PHE C 432 " pdb=" N PRO C 433 " pdb=" CA PRO C 433 " ideal model delta sigma weight residual 119.66 126.07 -6.41 7.20e-01 1.93e+00 7.93e+01 angle pdb=" C PHE B 432 " pdb=" N PRO B 433 " pdb=" CA PRO B 433 " ideal model delta sigma weight residual 119.66 126.07 -6.41 7.20e-01 1.93e+00 7.93e+01 angle pdb=" C PHE D 432 " pdb=" N PRO D 433 " pdb=" CA PRO D 433 " ideal model delta sigma weight residual 119.66 126.07 -6.41 7.20e-01 1.93e+00 7.93e+01 angle pdb=" C PHE A 432 " pdb=" N PRO A 433 " pdb=" CA PRO A 433 " ideal model delta sigma weight residual 119.66 126.07 -6.41 7.20e-01 1.93e+00 7.93e+01 angle pdb=" C LYS B 101 " pdb=" N PRO B 102 " pdb=" CA PRO B 102 " ideal model delta sigma weight residual 119.24 127.40 -8.16 1.04e+00 9.25e-01 6.16e+01 ... (remaining 21331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 9120 17.51 - 35.02: 252 35.02 - 52.53: 48 52.53 - 70.05: 32 70.05 - 87.56: 8 Dihedral angle restraints: 9460 sinusoidal: 3484 harmonic: 5976 Sorted by residual: dihedral pdb=" CB CYS A 188 " pdb=" SG CYS A 188 " pdb=" SG CYS A 604 " pdb=" CB CYS A 604 " ideal model delta sinusoidal sigma weight residual -86.00 -139.62 53.62 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CB CYS C 188 " pdb=" SG CYS C 188 " pdb=" SG CYS C 604 " pdb=" CB CYS C 604 " ideal model delta sinusoidal sigma weight residual -86.00 -139.62 53.62 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CB CYS B 188 " pdb=" SG CYS B 188 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 -139.62 53.62 1 1.00e+01 1.00e-02 3.91e+01 ... (remaining 9457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1712 0.058 - 0.116: 624 0.116 - 0.174: 136 0.174 - 0.232: 8 0.232 - 0.290: 4 Chirality restraints: 2484 Sorted by residual: chirality pdb=" C2 NAG A 701 " pdb=" C1 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" N2 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.49 -2.78 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C2 NAG D 701 " pdb=" C1 NAG D 701 " pdb=" C3 NAG D 701 " pdb=" N2 NAG D 701 " both_signs ideal model delta sigma weight residual False -2.49 -2.78 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C2 NAG B 701 " pdb=" C1 NAG B 701 " pdb=" C3 NAG B 701 " pdb=" N2 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.49 -2.78 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 2481 not shown) Planarity restraints: 2716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 571 " 0.043 2.00e-02 2.50e+03 2.21e-02 9.74e+00 pdb=" CG TYR A 571 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 571 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 571 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR A 571 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 571 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 571 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 571 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 571 " 0.043 2.00e-02 2.50e+03 2.21e-02 9.74e+00 pdb=" CG TYR D 571 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR D 571 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR D 571 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR D 571 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR D 571 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR D 571 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 571 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 571 " 0.043 2.00e-02 2.50e+03 2.21e-02 9.74e+00 pdb=" CG TYR C 571 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 571 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR C 571 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR C 571 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR C 571 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR C 571 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 571 " 0.029 2.00e-02 2.50e+03 ... (remaining 2713 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 4 2.47 - 3.08: 10244 3.08 - 3.69: 21203 3.69 - 4.29: 33243 4.29 - 4.90: 55526 Nonbonded interactions: 120220 Sorted by model distance: nonbonded pdb=" OD2 ASP C 544 " pdb="ZN ZN C 702 " model vdw 1.868 2.230 nonbonded pdb=" OD2 ASP D 544 " pdb="ZN ZN D 702 " model vdw 1.868 2.230 nonbonded pdb=" OD2 ASP A 544 " pdb="ZN ZN A 702 " model vdw 1.868 2.230 nonbonded pdb=" OD2 ASP B 544 " pdb="ZN ZN B 702 " model vdw 1.868 2.230 nonbonded pdb=" OG SER A 230 " pdb=" NH1 ARG A 257 " model vdw 2.546 3.120 ... (remaining 120215 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 45.180 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 : 0.012 0.065 15656 Z= 0.772 Angle : 1.272 8.162 21336 Z= 0.891 Chirality : 0.060 0.290 2484 Planarity : 0.008 0.126 2712 Dihedral : 10.007 87.557 5544 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.52 (0.17), residues: 2028 helix: 1.39 (0.26), residues: 316 sheet: 0.68 (0.17), residues: 780 loop : -0.24 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.005 TRP B 318 HIS 0.003 0.001 HIS C 596 PHE 0.020 0.005 PHE C 523 TYR 0.043 0.005 TYR A 571 ARG 0.005 0.001 ARG C 592 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.678 Fit side-chains REVERT: A 181 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7704 (mt-10) REVERT: B 181 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7689 (mt-10) REVERT: C 181 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7683 (mt-10) REVERT: D 181 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7691 (mt-10) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.3006 time to fit residues: 114.6681 Evaluate side-chains 140 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 185 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 GLN B 601 GLN C 601 GLN D 601 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15656 Z= 0.254 Angle : 0.546 4.465 21336 Z= 0.302 Chirality : 0.046 0.146 2484 Planarity : 0.004 0.039 2712 Dihedral : 4.789 21.380 2280 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.30 % Allowed : 3.63 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.95 (0.18), residues: 2028 helix: 2.92 (0.27), residues: 316 sheet: 0.83 (0.18), residues: 772 loop : -0.32 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 274 HIS 0.004 0.001 HIS B 194 PHE 0.019 0.002 PHE B 523 TYR 0.016 0.002 TYR D 446 ARG 0.002 0.000 ARG D 463 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 1.702 Fit side-chains REVERT: A 488 MET cc_start: 0.8247 (ttm) cc_final: 0.8006 (ttm) REVERT: A 520 ASP cc_start: 0.7069 (t0) cc_final: 0.6866 (t0) REVERT: B 488 MET cc_start: 0.8235 (ttm) cc_final: 0.8003 (ttm) REVERT: C 488 MET cc_start: 0.8234 (ttm) cc_final: 0.8003 (ttm) REVERT: D 488 MET cc_start: 0.8245 (ttm) cc_final: 0.8000 (ttm) REVERT: D 520 ASP cc_start: 0.7072 (t0) cc_final: 0.6870 (t0) outliers start: 20 outliers final: 16 residues processed: 168 average time/residue: 0.2649 time to fit residues: 66.7997 Evaluate side-chains 156 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 140 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 410 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 chunk 200 optimal weight: 0.2980 chunk 165 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8325 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15656 Z= 0.213 Angle : 0.488 4.484 21336 Z= 0.268 Chirality : 0.045 0.148 2484 Planarity : 0.004 0.039 2712 Dihedral : 4.397 17.227 2280 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.55 % Allowed : 3.89 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.87 (0.19), residues: 2028 helix: 3.37 (0.26), residues: 320 sheet: 0.71 (0.19), residues: 772 loop : -0.51 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 274 HIS 0.004 0.001 HIS D 194 PHE 0.017 0.002 PHE D 523 TYR 0.016 0.002 TYR B 446 ARG 0.002 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 1.826 Fit side-chains REVERT: A 520 ASP cc_start: 0.7126 (t0) cc_final: 0.6896 (t0) REVERT: D 520 ASP cc_start: 0.7125 (t0) cc_final: 0.6898 (t0) outliers start: 24 outliers final: 16 residues processed: 176 average time/residue: 0.2512 time to fit residues: 69.7852 Evaluate side-chains 144 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 410 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 124 optimal weight: 0.0020 chunk 186 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 97 optimal weight: 0.0980 chunk 176 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 GLN B 601 GLN C 601 GLN D 601 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15656 Z= 0.144 Angle : 0.455 4.614 21336 Z= 0.246 Chirality : 0.044 0.145 2484 Planarity : 0.003 0.036 2712 Dihedral : 4.136 17.089 2280 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.30 % Allowed : 5.96 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.89 (0.19), residues: 2028 helix: 3.62 (0.26), residues: 320 sheet: 0.73 (0.19), residues: 756 loop : -0.60 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 274 HIS 0.002 0.001 HIS C 312 PHE 0.014 0.002 PHE D 523 TYR 0.012 0.001 TYR D 446 ARG 0.001 0.000 ARG B 463 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 1.808 Fit side-chains REVERT: A 410 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8443 (mt) REVERT: A 520 ASP cc_start: 0.7193 (t0) cc_final: 0.6949 (t0) REVERT: B 410 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8444 (mt) REVERT: C 410 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8435 (mt) REVERT: D 410 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8439 (mt) REVERT: D 520 ASP cc_start: 0.7190 (t0) cc_final: 0.6946 (t0) outliers start: 20 outliers final: 16 residues processed: 156 average time/residue: 0.2707 time to fit residues: 63.6304 Evaluate side-chains 152 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 447 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.2980 chunk 111 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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: 0.8331 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15656 Z= 0.208 Angle : 0.472 4.573 21336 Z= 0.254 Chirality : 0.045 0.143 2484 Planarity : 0.004 0.036 2712 Dihedral : 4.138 16.601 2280 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.42 % Allowed : 5.83 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.83 (0.19), residues: 2028 helix: 3.65 (0.26), residues: 320 sheet: 0.72 (0.19), residues: 756 loop : -0.69 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 274 HIS 0.004 0.001 HIS A 312 PHE 0.015 0.002 PHE D 523 TYR 0.014 0.001 TYR C 446 ARG 0.002 0.000 ARG C 463 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 1.875 Fit side-chains REVERT: A 410 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8455 (mt) REVERT: A 520 ASP cc_start: 0.7122 (t0) cc_final: 0.6876 (t0) REVERT: B 410 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8454 (mt) REVERT: C 410 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8447 (mt) REVERT: D 410 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8450 (mt) REVERT: D 520 ASP cc_start: 0.7114 (t0) cc_final: 0.6870 (t0) outliers start: 22 outliers final: 18 residues processed: 160 average time/residue: 0.2559 time to fit residues: 63.7956 Evaluate side-chains 154 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 477 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.6980 chunk 177 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 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: 0.8362 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15656 Z= 0.288 Angle : 0.507 4.536 21336 Z= 0.273 Chirality : 0.046 0.148 2484 Planarity : 0.004 0.037 2712 Dihedral : 4.306 16.412 2280 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.88 % Allowed : 6.15 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.62 (0.19), residues: 2028 helix: 3.56 (0.26), residues: 320 sheet: 0.52 (0.19), residues: 748 loop : -0.78 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 274 HIS 0.004 0.001 HIS D 194 PHE 0.015 0.002 PHE D 523 TYR 0.017 0.002 TYR A 446 ARG 0.002 0.000 ARG D 463 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 124 time to evaluate : 2.365 Fit side-chains REVERT: A 410 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8501 (mt) REVERT: A 520 ASP cc_start: 0.7186 (t0) cc_final: 0.6951 (t0) REVERT: B 410 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8497 (mt) REVERT: C 410 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8492 (mt) REVERT: D 410 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8495 (mt) REVERT: D 520 ASP cc_start: 0.7184 (t0) cc_final: 0.6950 (t0) outliers start: 29 outliers final: 17 residues processed: 148 average time/residue: 0.2534 time to fit residues: 58.2125 Evaluate side-chains 145 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 477 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.1481 > 50: distance: 47 - 134: 5.558 distance: 50 - 131: 14.273 distance: 60 - 120: 18.909 distance: 62 - 67: 5.512 distance: 63 - 117: 10.674 distance: 67 - 68: 12.212 distance: 68 - 69: 12.970 distance: 68 - 71: 20.060 distance: 69 - 70: 11.268 distance: 69 - 75: 14.563 distance: 71 - 72: 14.800 distance: 72 - 73: 11.086 distance: 72 - 74: 10.877 distance: 75 - 76: 5.921 distance: 76 - 77: 18.295 distance: 76 - 79: 9.493 distance: 77 - 78: 22.635 distance: 77 - 84: 8.580 distance: 79 - 80: 16.228 distance: 80 - 81: 6.361 distance: 81 - 82: 15.246 distance: 82 - 83: 17.034 distance: 84 - 85: 4.553 distance: 86 - 87: 10.093 distance: 86 - 88: 24.681 distance: 88 - 89: 30.393 distance: 89 - 90: 7.778 distance: 89 - 92: 16.037 distance: 90 - 91: 15.416 distance: 90 - 97: 10.350 distance: 92 - 93: 16.916 distance: 93 - 94: 12.154 distance: 94 - 95: 22.873 distance: 94 - 96: 27.595 distance: 97 - 98: 23.874 distance: 98 - 99: 4.316 distance: 98 - 101: 25.921 distance: 99 - 100: 21.164 distance: 99 - 106: 13.402 distance: 101 - 102: 21.509 distance: 102 - 103: 34.307 distance: 103 - 104: 4.501 distance: 103 - 105: 9.307 distance: 106 - 107: 13.984 distance: 107 - 108: 4.383 distance: 108 - 109: 6.818 distance: 108 - 110: 3.693 distance: 110 - 111: 4.516 distance: 110 - 116: 18.088 distance: 111 - 112: 13.414 distance: 111 - 114: 11.340 distance: 112 - 113: 9.204 distance: 112 - 117: 9.871 distance: 114 - 115: 10.978 distance: 115 - 116: 21.125 distance: 117 - 118: 7.356 distance: 118 - 119: 19.797 distance: 118 - 121: 16.372 distance: 119 - 120: 20.421 distance: 119 - 126: 14.479 distance: 121 - 122: 6.595 distance: 122 - 123: 10.286 distance: 123 - 124: 12.742 distance: 123 - 125: 32.404 distance: 126 - 127: 7.971 distance: 127 - 128: 35.370 distance: 127 - 130: 27.318 distance: 128 - 129: 14.042 distance: 128 - 131: 11.670 distance: 131 - 132: 10.527 distance: 132 - 133: 10.814 distance: 132 - 135: 18.382 distance: 133 - 134: 6.053 distance: 133 - 137: 5.952 distance: 135 - 136: 17.054