Starting phenix.real_space_refine on Sun Jul 21 19:06:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvi_41643/07_2024/8tvi_41643_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvi_41643/07_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_41643/07_2024/8tvi_41643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvi_41643/07_2024/8tvi_41643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvi_41643/07_2024/8tvi_41643_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvi_41643/07_2024/8tvi_41643_neut.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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 9.32, 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: 5.51 Conformation dependent library (CDL) restraints added in 2.7 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: 1.73 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: 4.37 Time building geometry restraints manager: 6.19 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 2.520 ... (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 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: 6.930 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: 0.000 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 44.410 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.500 ------------------------------------------------------------------------------- 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 : 1.702 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: 0.3010 time to fit residues: 114.8339 Evaluate side-chains 140 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.681 ------------------------------------------------------------------------------- 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: 0.9980 chunk 154 optimal weight: 0.8980 chunk 85 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 159 optimal weight: 0.8980 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: 0.7180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 601 GLN D 601 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15656 Z= 0.239 Angle : 0.526 4.306 21336 Z= 0.294 Chirality : 0.045 0.144 2484 Planarity : 0.004 0.039 2712 Dihedral : 4.756 21.361 2280 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 1.11 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: 0.85 (0.18), residues: 772 loop : -0.33 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 274 HIS 0.003 0.001 HIS B 194 PHE 0.021 0.002 PHE B 523 TYR 0.015 0.002 TYR C 446 ARG 0.002 0.000 ARG C 398 *********************** 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 168 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 1.670 Fit side-chains REVERT: A 488 MET cc_start: 0.8231 (ttm) cc_final: 0.7991 (ttm) REVERT: B 488 MET cc_start: 0.8218 (ttm) cc_final: 0.7984 (ttm) REVERT: C 488 MET cc_start: 0.8216 (ttm) cc_final: 0.7983 (ttm) REVERT: D 488 MET cc_start: 0.8227 (ttm) cc_final: 0.7986 (ttm) outliers start: 20 outliers final: 16 residues processed: 160 average time/residue: 0.2717 time to fit residues: 64.9793 Evaluate side-chains 148 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.629 ------------------------------------------------------------------------------- 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: 0.3980 chunk 57 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 185 optimal weight: 0.0670 chunk 200 optimal weight: 0.4980 chunk 165 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 148 optimal weight: 0.4980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 601 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15656 Z= 0.144 Angle : 0.455 4.552 21336 Z= 0.249 Chirality : 0.044 0.145 2484 Planarity : 0.004 0.037 2712 Dihedral : 4.256 17.147 2280 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.30 % Allowed : 4.66 % Favored : 94.04 % 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: 1.04 (0.18), residues: 2028 helix: 3.51 (0.26), residues: 316 sheet: 0.84 (0.18), residues: 780 loop : -0.43 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 274 HIS 0.002 0.001 HIS B 194 PHE 0.013 0.002 PHE D 203 TYR 0.012 0.001 TYR B 446 ARG 0.001 0.000 ARG C 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 167 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 1.697 Fit side-chains REVERT: A 410 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8438 (mt) REVERT: A 474 SER cc_start: 0.8186 (p) cc_final: 0.7969 (m) REVERT: B 410 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8437 (mt) REVERT: B 474 SER cc_start: 0.8192 (p) cc_final: 0.7972 (m) REVERT: C 410 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8433 (mt) REVERT: C 474 SER cc_start: 0.8176 (p) cc_final: 0.7965 (m) REVERT: D 410 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8436 (mt) REVERT: D 474 SER cc_start: 0.8165 (p) cc_final: 0.7963 (m) outliers start: 20 outliers final: 12 residues processed: 163 average time/residue: 0.2563 time to fit residues: 65.6025 Evaluate side-chains 144 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 2.350 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 88 optimal weight: 0.0670 chunk 124 optimal weight: 0.8980 chunk 186 optimal weight: 0.7980 chunk 197 optimal weight: 3.9990 chunk 97 optimal weight: 0.3980 chunk 176 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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: 0.8306 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15656 Z= 0.173 Angle : 0.453 4.596 21336 Z= 0.246 Chirality : 0.044 0.140 2484 Planarity : 0.003 0.036 2712 Dihedral : 4.141 16.881 2280 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.04 % Allowed : 6.74 % Favored : 92.23 % 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: 0.99 (0.19), residues: 2028 helix: 3.63 (0.26), residues: 320 sheet: 0.80 (0.19), residues: 756 loop : -0.50 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 274 HIS 0.003 0.001 HIS C 194 PHE 0.015 0.002 PHE D 523 TYR 0.014 0.001 TYR B 446 ARG 0.001 0.000 ARG B 592 *********************** 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 165 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 1.712 Fit side-chains REVERT: A 132 TYR cc_start: 0.6535 (m-10) cc_final: 0.6312 (m-10) REVERT: A 410 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8422 (mt) REVERT: A 488 MET cc_start: 0.8296 (ttm) cc_final: 0.8058 (ttm) REVERT: B 132 TYR cc_start: 0.6536 (m-10) cc_final: 0.6312 (m-10) REVERT: B 410 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8418 (mt) REVERT: B 488 MET cc_start: 0.8287 (ttm) cc_final: 0.8047 (ttm) REVERT: C 132 TYR cc_start: 0.6536 (m-10) cc_final: 0.6315 (m-10) REVERT: C 410 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8418 (mt) REVERT: C 488 MET cc_start: 0.8288 (ttm) cc_final: 0.8046 (ttm) REVERT: D 132 TYR cc_start: 0.6537 (m-10) cc_final: 0.6315 (m-10) REVERT: D 410 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8418 (mt) REVERT: D 488 MET cc_start: 0.8295 (ttm) cc_final: 0.8055 (ttm) outliers start: 16 outliers final: 12 residues processed: 161 average time/residue: 0.2555 time to fit residues: 63.3968 Evaluate side-chains 136 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.582 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 0.0670 chunk 176 optimal weight: 0.9980 chunk 49 optimal weight: 0.1980 overall best weight: 0.8320 ------------------------------------------------------------------------------- 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: 0.8336 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15656 Z= 0.229 Angle : 0.482 4.541 21336 Z= 0.259 Chirality : 0.045 0.144 2484 Planarity : 0.004 0.036 2712 Dihedral : 4.217 16.662 2280 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.68 % Allowed : 6.35 % 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: 0.85 (0.19), residues: 2028 helix: 3.68 (0.26), residues: 320 sheet: 0.71 (0.19), residues: 748 loop : -0.66 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 274 HIS 0.004 0.001 HIS C 312 PHE 0.014 0.002 PHE B 523 TYR 0.015 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 154 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 1.749 Fit side-chains REVERT: A 410 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8398 (mt) REVERT: B 410 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8394 (mt) REVERT: C 410 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8393 (mt) REVERT: D 410 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8395 (mt) outliers start: 26 outliers final: 18 residues processed: 148 average time/residue: 0.2508 time to fit residues: 57.2654 Evaluate side-chains 143 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 1.782 ------------------------------------------------------------------------------- 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 135 GLU Chi-restraints excluded: chain A residue 201 VAL 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 135 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 410 ILE 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 201 VAL 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 135 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 410 ILE 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: 5.9990 chunk 177 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 91 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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: 0.8355 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15656 Z= 0.256 Angle : 0.499 4.541 21336 Z= 0.267 Chirality : 0.045 0.145 2484 Planarity : 0.004 0.035 2712 Dihedral : 4.277 16.417 2280 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.49 % Allowed : 7.58 % Favored : 90.93 % 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: 0.68 (0.19), residues: 2028 helix: 3.69 (0.26), residues: 320 sheet: 0.52 (0.19), residues: 748 loop : -0.73 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 274 HIS 0.005 0.001 HIS A 312 PHE 0.014 0.002 PHE A 523 TYR 0.016 0.002 TYR B 446 ARG 0.002 0.000 ARG C 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 147 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 1.683 Fit side-chains outliers start: 23 outliers final: 19 residues processed: 140 average time/residue: 0.2544 time to fit residues: 54.5595 Evaluate side-chains 143 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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 135 GLU Chi-restraints excluded: chain A residue 201 VAL 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 201 VAL Chi-restraints excluded: chain B residue 477 SER 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 477 SER Chi-restraints excluded: chain D residue 86 LEU 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 477 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8345 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15656 Z= 0.211 Angle : 0.473 4.544 21336 Z= 0.254 Chirality : 0.045 0.144 2484 Planarity : 0.003 0.033 2712 Dihedral : 4.184 16.216 2280 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.55 % Allowed : 7.71 % Favored : 90.74 % 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: 0.65 (0.19), residues: 2028 helix: 3.72 (0.26), residues: 320 sheet: 0.50 (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 0.003 0.001 HIS D 194 PHE 0.014 0.002 PHE B 523 TYR 0.014 0.001 TYR B 446 ARG 0.001 0.000 ARG D 463 *********************** REFINEMENT MACRO_CYCLE 7 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 152 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 1.813 Fit side-chains outliers start: 24 outliers final: 20 residues processed: 144 average time/residue: 0.2653 time to fit residues: 59.3272 Evaluate side-chains 144 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 1.666 ------------------------------------------------------------------------------- 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 135 GLU Chi-restraints excluded: chain A residue 201 VAL 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 201 VAL 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 201 VAL Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain D residue 86 LEU 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 477 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 125 optimal weight: 0.0980 chunk 133 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 154 optimal weight: 8.9990 chunk 178 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15656 Z= 0.166 Angle : 0.447 4.590 21336 Z= 0.239 Chirality : 0.044 0.141 2484 Planarity : 0.003 0.032 2712 Dihedral : 4.016 14.980 2280 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.23 % Allowed : 9.07 % Favored : 89.70 % 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: 0.73 (0.19), residues: 2028 helix: 3.82 (0.26), residues: 320 sheet: 0.57 (0.20), residues: 748 loop : -0.77 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 274 HIS 0.002 0.001 HIS D 194 PHE 0.015 0.002 PHE C 523 TYR 0.012 0.001 TYR B 446 ARG 0.001 0.000 ARG D 398 *********************** REFINEMENT MACRO_CYCLE 8 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 147 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.583 Fit side-chains outliers start: 19 outliers final: 19 residues processed: 140 average time/residue: 0.2579 time to fit residues: 55.1080 Evaluate side-chains 139 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 1.797 ------------------------------------------------------------------------------- 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 135 GLU Chi-restraints excluded: chain A residue 201 VAL 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 201 VAL Chi-restraints excluded: chain B residue 477 SER 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 477 SER Chi-restraints excluded: chain D residue 86 LEU 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 477 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.5980 chunk 171 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 165 optimal weight: 4.9990 chunk 173 optimal weight: 0.1980 chunk 182 optimal weight: 0.4980 chunk 120 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.8324 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15656 Z= 0.155 Angle : 0.438 4.598 21336 Z= 0.234 Chirality : 0.044 0.140 2484 Planarity : 0.003 0.032 2712 Dihedral : 3.930 14.714 2280 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.04 % Allowed : 9.26 % Favored : 89.70 % 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: 0.81 (0.19), residues: 2028 helix: 3.93 (0.26), residues: 320 sheet: 0.62 (0.20), residues: 748 loop : -0.74 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 274 HIS 0.002 0.001 HIS B 194 PHE 0.013 0.002 PHE C 523 TYR 0.012 0.001 TYR B 446 ARG 0.000 0.000 ARG B 398 *********************** REFINEMENT MACRO_CYCLE 9 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 148 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.663 Fit side-chains outliers start: 16 outliers final: 16 residues processed: 140 average time/residue: 0.2597 time to fit residues: 55.5386 Evaluate side-chains 140 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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 135 GLU 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 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 477 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 477 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 134 optimal weight: 0.5980 chunk 203 optimal weight: 2.9990 chunk 187 optimal weight: 0.6980 chunk 161 optimal weight: 0.0070 chunk 16 optimal weight: 0.7980 chunk 125 optimal weight: 0.0570 chunk 99 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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: 0.8311 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15656 Z= 0.137 Angle : 0.428 4.608 21336 Z= 0.228 Chirality : 0.044 0.138 2484 Planarity : 0.003 0.031 2712 Dihedral : 3.807 14.798 2280 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.04 % Allowed : 9.52 % Favored : 89.44 % 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: 4.01 (0.26), residues: 320 sheet: 0.62 (0.20), residues: 748 loop : -0.72 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 274 HIS 0.002 0.000 HIS A 194 PHE 0.013 0.001 PHE B 523 TYR 0.011 0.001 TYR B 446 ARG 0.001 0.000 ARG D 463 ********************** REFINEMENT MACRO_CYCLE 10 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 139 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.747 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 132 average time/residue: 0.2695 time to fit residues: 53.7759 Evaluate side-chains 145 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 1.718 ------------------------------------------------------------------------------- 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 477 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 477 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.0040 chunk 142 optimal weight: 2.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 GLN D 430 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.118036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.090372 restraints weight = 18047.689| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.87 r_work: 0.2765 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2646 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= 0.199 Angle : 0.462 4.563 21336 Z= 0.247 Chirality : 0.044 0.144 2484 Planarity : 0.003 0.033 2712 Dihedral : 3.921 14.558 2280 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.97 % Allowed : 9.84 % Favored : 89.18 % 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: 0.79 (0.19), residues: 2028 helix: 3.96 (0.26), residues: 320 sheet: 0.60 (0.20), residues: 748 loop : -0.76 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 274 HIS 0.003 0.001 HIS C 194 PHE 0.014 0.002 PHE A 523 TYR 0.014 0.001 TYR D 446 ARG 0.001 0.000 ARG C 463 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3354.00 seconds wall clock time: 60 minutes 36.75 seconds (3636.75 seconds total)