Starting phenix.real_space_refine on Sat Feb 17 03:18:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n16_24114/02_2024/7n16_24114_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n16_24114/02_2024/7n16_24114.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/7n16_24114/02_2024/7n16_24114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n16_24114/02_2024/7n16_24114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n16_24114/02_2024/7n16_24114_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n16_24114/02_2024/7n16_24114_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.092 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 96 5.16 5 Na 1 4.78 5 C 11300 2.51 5 N 2860 2.21 5 O 3088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 106": "NH1" <-> "NH2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 158": "NH1" <-> "NH2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 229": "OD1" <-> "OD2" Residue "D TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 253": "OD1" <-> "OD2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 308": "NH1" <-> "NH2" Residue "D TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D GLU 423": "OE1" <-> "OE2" Residue "D PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 429": "OD1" <-> "OD2" Residue "D TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 453": "OD1" <-> "OD2" Residue "D ASP 464": "OD1" <-> "OD2" Residue "D GLU 504": "OE1" <-> "OE2" Residue "D ARG 528": "NH1" <-> "NH2" Residue "D GLU 529": "OE1" <-> "OE2" Residue "D ARG 537": "NH1" <-> "NH2" Residue "D PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 574": "NH1" <-> "NH2" Residue "D ARG 580": "NH1" <-> "NH2" Residue "D PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 594": "OD1" <-> "OD2" Residue "D ARG 600": "NH1" <-> "NH2" Residue "D GLU 601": "OE1" <-> "OE2" Residue "D ASP 604": "OD1" <-> "OD2" Residue "D ARG 614": "NH1" <-> "NH2" Residue "D GLU 615": "OE1" <-> "OE2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 429": "OD1" <-> "OD2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 453": "OD1" <-> "OD2" Residue "A ASP 464": "OD1" <-> "OD2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A GLU 529": "OE1" <-> "OE2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 594": "OD1" <-> "OD2" Residue "A ARG 600": "NH1" <-> "NH2" Residue "A GLU 601": "OE1" <-> "OE2" Residue "A ASP 604": "OD1" <-> "OD2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A GLU 615": "OE1" <-> "OE2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "B TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 229": "OD1" <-> "OD2" Residue "B TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 253": "OD1" <-> "OD2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 429": "OD1" <-> "OD2" Residue "B TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 453": "OD1" <-> "OD2" Residue "B ASP 464": "OD1" <-> "OD2" Residue "B GLU 504": "OE1" <-> "OE2" Residue "B ARG 528": "NH1" <-> "NH2" Residue "B GLU 529": "OE1" <-> "OE2" Residue "B ARG 537": "NH1" <-> "NH2" Residue "B PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 574": "NH1" <-> "NH2" Residue "B ARG 580": "NH1" <-> "NH2" Residue "B PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 594": "OD1" <-> "OD2" Residue "B ARG 600": "NH1" <-> "NH2" Residue "B GLU 601": "OE1" <-> "OE2" Residue "B ASP 604": "OD1" <-> "OD2" Residue "B ARG 614": "NH1" <-> "NH2" Residue "B GLU 615": "OE1" <-> "OE2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 253": "OD1" <-> "OD2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 429": "OD1" <-> "OD2" Residue "C TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 453": "OD1" <-> "OD2" Residue "C ASP 464": "OD1" <-> "OD2" Residue "C GLU 504": "OE1" <-> "OE2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C GLU 529": "OE1" <-> "OE2" Residue "C ARG 537": "NH1" <-> "NH2" Residue "C PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 574": "NH1" <-> "NH2" Residue "C ARG 580": "NH1" <-> "NH2" Residue "C PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 594": "OD1" <-> "OD2" Residue "C ARG 600": "NH1" <-> "NH2" Residue "C GLU 601": "OE1" <-> "OE2" Residue "C ASP 604": "OD1" <-> "OD2" Residue "C ARG 614": "NH1" <-> "NH2" Residue "C GLU 615": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17357 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 4252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4252 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 15, 'TRANS': 498} Chain breaks: 1 Chain: "A" Number of atoms: 4252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4252 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 15, 'TRANS': 498} Chain breaks: 1 Chain: "B" Number of atoms: 4252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4252 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 15, 'TRANS': 498} Chain breaks: 1 Chain: "C" Number of atoms: 4252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4252 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 15, 'TRANS': 498} Chain breaks: 1 Chain: "D" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 87 Unusual residues: {'CPL': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-4': 4, 'CPL:plan-3': 4, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 88 Unusual residues: {' NA': 1, 'CPL': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-4': 4, 'CPL:plan-3': 4, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 87 Unusual residues: {'CPL': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-4': 4, 'CPL:plan-3': 4, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 87 Unusual residues: {'CPL': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-4': 4, 'CPL:plan-3': 4, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 38 Time building chain proxies: 10.20, per 1000 atoms: 0.59 Number of scatterers: 17357 At special positions: 0 Unit cell: (133.63, 133.63, 136.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 12 15.00 Na 1 11.00 O 3088 8.00 N 2860 7.00 C 11300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 172 " distance=2.03 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 172 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 172 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.59 Conformation dependent library (CDL) restraints added in 3.1 seconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3896 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 12 sheets defined 52.9% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'D' and resid 105 through 110 Processing helix chain 'D' and resid 119 through 144 Processing helix chain 'D' and resid 198 through 223 Processing helix chain 'D' and resid 237 through 246 Processing helix chain 'D' and resid 249 through 257 removed outlier: 3.905A pdb=" N LEU D 257 " --> pdb=" O ASP D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 261 No H-bonds generated for 'chain 'D' and resid 259 through 261' Processing helix chain 'D' and resid 279 through 285 removed outlier: 4.089A pdb=" N ASN D 282 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG D 283 " --> pdb=" O ARG D 280 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE D 285 " --> pdb=" O ASN D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 299 Processing helix chain 'D' and resid 304 through 334 Processing helix chain 'D' and resid 359 through 374 Processing helix chain 'D' and resid 386 through 417 removed outlier: 3.522A pdb=" N MET D 417 " --> pdb=" O MET D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 438 Processing helix chain 'D' and resid 442 through 457 Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 473 through 488 removed outlier: 4.026A pdb=" N VAL D 483 " --> pdb=" O ILE D 479 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE D 485 " --> pdb=" O MET D 481 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR D 487 " --> pdb=" O VAL D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 508 removed outlier: 3.676A pdb=" N LYS D 508 " --> pdb=" O GLU D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 600 Processing helix chain 'D' and resid 603 through 619 Processing helix chain 'A' and resid 105 through 110 Processing helix chain 'A' and resid 119 through 144 Processing helix chain 'A' and resid 198 through 223 Processing helix chain 'A' and resid 237 through 246 Processing helix chain 'A' and resid 249 through 257 removed outlier: 3.905A pdb=" N LEU A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 279 through 285 removed outlier: 4.089A pdb=" N ASN A 282 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 285 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 299 Processing helix chain 'A' and resid 304 through 334 Processing helix chain 'A' and resid 359 through 374 Processing helix chain 'A' and resid 386 through 417 removed outlier: 3.522A pdb=" N MET A 417 " --> pdb=" O MET A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 438 Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 473 through 488 removed outlier: 4.026A pdb=" N VAL A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 485 " --> pdb=" O MET A 481 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.676A pdb=" N LYS A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 600 Processing helix chain 'A' and resid 603 through 619 Processing helix chain 'B' and resid 105 through 110 Processing helix chain 'B' and resid 119 through 144 Processing helix chain 'B' and resid 198 through 223 Processing helix chain 'B' and resid 237 through 246 Processing helix chain 'B' and resid 249 through 257 removed outlier: 3.905A pdb=" N LEU B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 279 through 285 removed outlier: 4.088A pdb=" N ASN B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG B 283 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 285 " --> pdb=" O ASN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 299 Processing helix chain 'B' and resid 304 through 334 Processing helix chain 'B' and resid 359 through 374 Processing helix chain 'B' and resid 386 through 417 removed outlier: 3.522A pdb=" N MET B 417 " --> pdb=" O MET B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 438 Processing helix chain 'B' and resid 442 through 457 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 473 through 488 removed outlier: 4.026A pdb=" N VAL B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 485 " --> pdb=" O MET B 481 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR B 487 " --> pdb=" O VAL B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 508 removed outlier: 3.677A pdb=" N LYS B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 600 Processing helix chain 'B' and resid 603 through 619 Processing helix chain 'C' and resid 105 through 110 Processing helix chain 'C' and resid 119 through 144 Processing helix chain 'C' and resid 198 through 223 Processing helix chain 'C' and resid 237 through 246 Processing helix chain 'C' and resid 249 through 257 removed outlier: 3.904A pdb=" N LEU C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 279 through 285 removed outlier: 4.089A pdb=" N ASN C 282 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG C 283 " --> pdb=" O ARG C 280 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE C 285 " --> pdb=" O ASN C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 299 Processing helix chain 'C' and resid 304 through 334 Processing helix chain 'C' and resid 359 through 374 Processing helix chain 'C' and resid 386 through 417 removed outlier: 3.522A pdb=" N MET C 417 " --> pdb=" O MET C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 438 Processing helix chain 'C' and resid 442 through 457 Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 488 removed outlier: 4.026A pdb=" N VAL C 483 " --> pdb=" O ILE C 479 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE C 485 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 508 removed outlier: 3.676A pdb=" N LYS C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 600 Processing helix chain 'C' and resid 603 through 619 Processing sheet with id= A, first strand: chain 'D' and resid 185 through 188 Processing sheet with id= B, first strand: chain 'D' and resid 510 through 514 removed outlier: 3.525A pdb=" N THR D 585 " --> pdb=" O PHE D 514 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 538 through 540 Processing sheet with id= D, first strand: chain 'A' and resid 185 through 188 Processing sheet with id= E, first strand: chain 'A' and resid 510 through 514 removed outlier: 3.525A pdb=" N THR A 585 " --> pdb=" O PHE A 514 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 538 through 540 Processing sheet with id= G, first strand: chain 'B' and resid 185 through 188 Processing sheet with id= H, first strand: chain 'B' and resid 510 through 514 removed outlier: 3.525A pdb=" N THR B 585 " --> pdb=" O PHE B 514 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 538 through 540 Processing sheet with id= J, first strand: chain 'C' and resid 185 through 188 Processing sheet with id= K, first strand: chain 'C' and resid 510 through 514 removed outlier: 3.524A pdb=" N THR C 585 " --> pdb=" O PHE C 514 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 538 through 540 852 hydrogen bonds defined for protein. 2520 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: 4.70 Time building geometry restraints manager: 7.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2672 1.30 - 1.43: 4990 1.43 - 1.56: 9906 1.56 - 1.68: 32 1.68 - 1.81: 156 Bond restraints: 17756 Sorted by residual: bond pdb=" C11 CPL B1804 " pdb=" O3 CPL B1804 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C11 CPL D 803 " pdb=" O3 CPL D 803 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C11 CPL C1804 " pdb=" O3 CPL C1804 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C11 CPL A1804 " pdb=" O3 CPL A1804 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C11 CPL C1801 " pdb=" O3 CPL C1801 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 17751 not shown) Histogram of bond angle deviations from ideal: 96.89 - 104.40: 206 104.40 - 111.91: 7984 111.91 - 119.42: 6857 119.42 - 126.93: 8709 126.93 - 134.44: 280 Bond angle restraints: 24036 Sorted by residual: angle pdb=" O3P CPL B1801 " pdb=" P CPL B1801 " pdb=" O4P CPL B1801 " ideal model delta sigma weight residual 93.29 111.26 -17.97 3.00e+00 1.11e-01 3.59e+01 angle pdb=" O3P CPL C1801 " pdb=" P CPL C1801 " pdb=" O4P CPL C1801 " ideal model delta sigma weight residual 93.29 111.24 -17.95 3.00e+00 1.11e-01 3.58e+01 angle pdb=" O3P CPL A1801 " pdb=" P CPL A1801 " pdb=" O4P CPL A1801 " ideal model delta sigma weight residual 93.29 111.23 -17.94 3.00e+00 1.11e-01 3.57e+01 angle pdb=" O3P CPL D 804 " pdb=" P CPL D 804 " pdb=" O4P CPL D 804 " ideal model delta sigma weight residual 93.29 111.21 -17.92 3.00e+00 1.11e-01 3.57e+01 angle pdb=" O3P CPL C1804 " pdb=" P CPL C1804 " pdb=" O4P CPL C1804 " ideal model delta sigma weight residual 93.29 110.02 -16.73 3.00e+00 1.11e-01 3.11e+01 ... (remaining 24031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 10236 35.11 - 70.23: 272 70.23 - 105.34: 20 105.34 - 140.46: 16 140.46 - 175.57: 12 Dihedral angle restraints: 10556 sinusoidal: 4488 harmonic: 6068 Sorted by residual: dihedral pdb=" CA ASP A 191 " pdb=" C ASP A 191 " pdb=" N LEU A 192 " pdb=" CA LEU A 192 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ASP D 191 " pdb=" C ASP D 191 " pdb=" N LEU D 192 " pdb=" CA LEU D 192 " ideal model delta harmonic sigma weight residual -180.00 -154.32 -25.68 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ASP C 191 " pdb=" C ASP C 191 " pdb=" N LEU C 192 " pdb=" CA LEU C 192 " ideal model delta harmonic sigma weight residual -180.00 -154.34 -25.66 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 10553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1685 0.049 - 0.098: 715 0.098 - 0.147: 154 0.147 - 0.196: 33 0.196 - 0.245: 37 Chirality restraints: 2624 Sorted by residual: chirality pdb=" CB VAL A 170 " pdb=" CA VAL A 170 " pdb=" CG1 VAL A 170 " pdb=" CG2 VAL A 170 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB VAL C 170 " pdb=" CA VAL C 170 " pdb=" CG1 VAL C 170 " pdb=" CG2 VAL C 170 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CB VAL B 170 " pdb=" CA VAL B 170 " pdb=" CG1 VAL B 170 " pdb=" CG2 VAL B 170 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 2621 not shown) Planarity restraints: 2948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 380 " -0.046 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO C 381 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 381 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 381 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 380 " 0.046 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO A 381 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 381 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 381 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 380 " 0.046 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO B 381 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 381 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 381 " 0.038 5.00e-02 4.00e+02 ... (remaining 2945 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3241 2.77 - 3.30: 14858 3.30 - 3.83: 29553 3.83 - 4.37: 33469 4.37 - 4.90: 57917 Nonbonded interactions: 139038 Sorted by model distance: nonbonded pdb=" O ASP A 191 " pdb=" OD1 ASP A 191 " model vdw 2.235 3.040 nonbonded pdb=" O ASP C 191 " pdb=" OD1 ASP C 191 " model vdw 2.235 3.040 nonbonded pdb=" O ASP D 191 " pdb=" OD1 ASP D 191 " model vdw 2.235 3.040 nonbonded pdb=" O ASP B 191 " pdb=" OD1 ASP B 191 " model vdw 2.235 3.040 nonbonded pdb=" O SER B 562 " pdb=" OG SER B 562 " model vdw 2.339 2.440 ... (remaining 139033 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' and (resid 104 through 620 or resid 1801 or (resid 1803 and (name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17)) or (resid 1804 an \ d (name C1 or name C11 or name C12 or name C13 or name C14 or name C2 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name O11 or name O1P or name \ O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'B' and (resid 104 through 620 or resid 1801 or (resid 1803 and (name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17)) or (resid 1804 an \ d (name C1 or name C11 or name C12 or name C13 or name C14 or name C2 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name O11 or name O1P or name \ O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'C' and (resid 104 through 620 or resid 1801 or (resid 1803 and (name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17)) or (resid 1804 an \ d (name C1 or name C11 or name C12 or name C13 or name C14 or name C2 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name O11 or name O1P or name \ O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'D' and (resid 104 through 620 or (resid 801 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C4 or name C5 or name O11 or name O1P or name O2 \ or name O2P or name O3 or name O31 or name O3P or name O4P or name P )) or (resi \ d 803 and (name C12 or name C13 or name C14 or name C15 or name C16 or name C17) \ ) or (resid 804 and (name C1 or name C11 or name C12 or name C13 or name C14 or \ name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name O11 o \ r name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P \ or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.700 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 47.840 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.090 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 17756 Z= 0.528 Angle : 1.179 17.974 24036 Z= 0.601 Chirality : 0.061 0.245 2624 Planarity : 0.008 0.068 2948 Dihedral : 18.872 175.569 6648 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.86 % Allowed : 9.87 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.13), residues: 2040 helix: -3.33 (0.09), residues: 1140 sheet: -0.52 (0.45), residues: 120 loop : -2.64 (0.18), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 266 HIS 0.004 0.001 HIS C 321 PHE 0.028 0.003 PHE B 145 TYR 0.026 0.003 TYR D 363 ARG 0.005 0.001 ARG B 447 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 322 time to evaluate : 2.040 Fit side-chains REVERT: D 159 PHE cc_start: 0.8226 (t80) cc_final: 0.7886 (t80) REVERT: D 272 ASN cc_start: 0.8215 (m-40) cc_final: 0.7987 (t0) REVERT: D 424 PHE cc_start: 0.7779 (t80) cc_final: 0.7478 (t80) REVERT: D 525 ASP cc_start: 0.7881 (t0) cc_final: 0.7484 (t0) REVERT: D 535 ARG cc_start: 0.7785 (ttm110) cc_final: 0.7474 (ptp-110) REVERT: D 558 PHE cc_start: 0.6782 (t80) cc_final: 0.6541 (t80) REVERT: A 159 PHE cc_start: 0.8196 (t80) cc_final: 0.7864 (t80) REVERT: A 272 ASN cc_start: 0.8224 (m-40) cc_final: 0.8008 (t0) REVERT: A 458 ASN cc_start: 0.8112 (t0) cc_final: 0.7899 (t0) REVERT: A 525 ASP cc_start: 0.7807 (t0) cc_final: 0.7339 (t0) REVERT: A 535 ARG cc_start: 0.7776 (ttm110) cc_final: 0.7485 (ptp-110) REVERT: A 558 PHE cc_start: 0.6771 (t80) cc_final: 0.6552 (t80) REVERT: B 159 PHE cc_start: 0.8240 (t80) cc_final: 0.7889 (t80) REVERT: B 525 ASP cc_start: 0.7853 (t0) cc_final: 0.7475 (t0) REVERT: B 535 ARG cc_start: 0.7814 (ttm110) cc_final: 0.7481 (ptp-110) REVERT: B 558 PHE cc_start: 0.6843 (t80) cc_final: 0.6567 (t80) REVERT: C 159 PHE cc_start: 0.8188 (t80) cc_final: 0.7870 (t80) REVERT: C 272 ASN cc_start: 0.8251 (m-40) cc_final: 0.8040 (t0) REVERT: C 413 MET cc_start: 0.7802 (tmm) cc_final: 0.7575 (ttp) REVERT: C 421 TRP cc_start: 0.6328 (t-100) cc_final: 0.5977 (t-100) REVERT: C 525 ASP cc_start: 0.7829 (t0) cc_final: 0.7524 (t0) REVERT: C 535 ARG cc_start: 0.7833 (ttm110) cc_final: 0.7464 (ptp-110) outliers start: 16 outliers final: 0 residues processed: 338 average time/residue: 0.3576 time to fit residues: 170.8639 Evaluate side-chains 236 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 2.007 ------------------------------------------------------------------------------- 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: 0.9990 chunk 154 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 30.0000 chunk 119 optimal weight: 0.3980 chunk 185 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 GLN D 188 GLN D 199 HIS D 416 ASN D 433 GLN D 458 ASN D 484 HIS D 510 GLN D 539 GLN A 114 GLN A 188 GLN A 199 HIS A 416 ASN A 433 GLN A 484 HIS A 539 GLN B 114 GLN B 188 GLN B 199 HIS B 416 ASN B 433 GLN B 458 ASN B 484 HIS B 510 GLN B 539 GLN C 114 GLN C 188 GLN C 199 HIS C 323 ASN C 416 ASN C 433 GLN C 458 ASN C 484 HIS C 510 GLN C 539 GLN C 578 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17756 Z= 0.173 Angle : 0.536 7.633 24036 Z= 0.277 Chirality : 0.039 0.136 2624 Planarity : 0.004 0.040 2948 Dihedral : 15.852 176.057 2564 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.50 % Allowed : 14.86 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.16), residues: 2040 helix: -0.82 (0.14), residues: 1144 sheet: -0.86 (0.40), residues: 120 loop : -2.28 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 329 HIS 0.001 0.000 HIS D 199 PHE 0.014 0.001 PHE B 138 TYR 0.013 0.001 TYR B 108 ARG 0.003 0.000 ARG C 528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 263 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7797 (p0) REVERT: D 146 ASN cc_start: 0.8076 (t0) cc_final: 0.7492 (t0) REVERT: D 182 GLU cc_start: 0.8314 (pm20) cc_final: 0.7790 (pm20) REVERT: D 272 ASN cc_start: 0.8233 (m-40) cc_final: 0.8023 (t0) REVERT: D 525 ASP cc_start: 0.7787 (t0) cc_final: 0.7278 (t70) REVERT: D 535 ARG cc_start: 0.7788 (ttm110) cc_final: 0.7303 (ptp-110) REVERT: A 115 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7823 (p0) REVERT: A 146 ASN cc_start: 0.8076 (t0) cc_final: 0.7494 (t0) REVERT: A 182 GLU cc_start: 0.8316 (pm20) cc_final: 0.7789 (pm20) REVERT: A 272 ASN cc_start: 0.8231 (m-40) cc_final: 0.8026 (t0) REVERT: A 525 ASP cc_start: 0.7724 (t0) cc_final: 0.7343 (t70) REVERT: A 535 ARG cc_start: 0.7818 (ttm110) cc_final: 0.7340 (ptp-110) REVERT: B 115 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7773 (p0) REVERT: B 146 ASN cc_start: 0.8164 (t0) cc_final: 0.7565 (t0) REVERT: B 507 LEU cc_start: 0.8243 (mm) cc_final: 0.8040 (mm) REVERT: B 525 ASP cc_start: 0.7795 (t0) cc_final: 0.7337 (t70) REVERT: B 558 PHE cc_start: 0.6886 (t80) cc_final: 0.6673 (t80) REVERT: C 115 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7806 (p0) REVERT: C 146 ASN cc_start: 0.8101 (t0) cc_final: 0.7511 (t0) REVERT: C 182 GLU cc_start: 0.8316 (pm20) cc_final: 0.7795 (pm20) REVERT: C 525 ASP cc_start: 0.7806 (t0) cc_final: 0.7499 (t70) REVERT: C 558 PHE cc_start: 0.6840 (t80) cc_final: 0.6554 (t80) outliers start: 28 outliers final: 21 residues processed: 284 average time/residue: 0.3080 time to fit residues: 128.0969 Evaluate side-chains 262 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 237 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 578 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 458 ASN B 349 GLN B 458 ASN C 323 ASN C 458 ASN C 578 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 17756 Z= 0.356 Angle : 0.606 8.913 24036 Z= 0.312 Chirality : 0.042 0.162 2624 Planarity : 0.004 0.039 2948 Dihedral : 14.683 174.363 2564 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.25 % Allowed : 16.85 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.17), residues: 2040 helix: 0.08 (0.15), residues: 1152 sheet: -1.26 (0.41), residues: 104 loop : -2.16 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 329 HIS 0.003 0.001 HIS B 199 PHE 0.019 0.002 PHE A 138 TYR 0.020 0.001 TYR A 363 ARG 0.004 0.000 ARG C 606 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 240 time to evaluate : 2.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 146 ASN cc_start: 0.8210 (t0) cc_final: 0.7628 (t0) REVERT: D 182 GLU cc_start: 0.8355 (pm20) cc_final: 0.7785 (pm20) REVERT: D 272 ASN cc_start: 0.8260 (m-40) cc_final: 0.8013 (t0) REVERT: D 525 ASP cc_start: 0.7818 (t0) cc_final: 0.7427 (t70) REVERT: A 146 ASN cc_start: 0.8209 (t0) cc_final: 0.7628 (t0) REVERT: A 272 ASN cc_start: 0.8256 (m-40) cc_final: 0.8016 (t0) REVERT: A 525 ASP cc_start: 0.7817 (t0) cc_final: 0.7404 (t70) REVERT: A 537 ARG cc_start: 0.7568 (ttm170) cc_final: 0.7324 (ttm110) REVERT: B 146 ASN cc_start: 0.8263 (t0) cc_final: 0.7622 (t0) REVERT: B 507 LEU cc_start: 0.8219 (mm) cc_final: 0.8011 (mm) REVERT: B 525 ASP cc_start: 0.7833 (t0) cc_final: 0.7472 (t70) REVERT: B 558 PHE cc_start: 0.6972 (t80) cc_final: 0.6720 (t80) REVERT: C 146 ASN cc_start: 0.8225 (t0) cc_final: 0.7647 (t0) REVERT: C 182 GLU cc_start: 0.8344 (pm20) cc_final: 0.7763 (pm20) REVERT: C 421 TRP cc_start: 0.6578 (t-100) cc_final: 0.6376 (t-100) REVERT: C 525 ASP cc_start: 0.7862 (t0) cc_final: 0.7506 (t70) REVERT: C 558 PHE cc_start: 0.6906 (t80) cc_final: 0.6664 (t80) outliers start: 42 outliers final: 28 residues processed: 272 average time/residue: 0.3087 time to fit residues: 125.3945 Evaluate side-chains 263 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 235 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 540 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 197 optimal weight: 9.9990 chunk 97 optimal weight: 0.0770 chunk 176 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 overall best weight: 1.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 458 ASN B 458 ASN C 458 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17756 Z= 0.216 Angle : 0.514 8.128 24036 Z= 0.266 Chirality : 0.039 0.147 2624 Planarity : 0.004 0.038 2948 Dihedral : 13.754 171.636 2564 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.36 % Allowed : 17.49 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.18), residues: 2040 helix: 0.70 (0.16), residues: 1148 sheet: -1.08 (0.39), residues: 128 loop : -2.04 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 421 HIS 0.002 0.001 HIS D 199 PHE 0.019 0.001 PHE B 159 TYR 0.013 0.001 TYR C 363 ARG 0.005 0.000 ARG C 606 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 247 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 146 ASN cc_start: 0.8004 (t0) cc_final: 0.7445 (t0) REVERT: D 182 GLU cc_start: 0.8311 (pm20) cc_final: 0.7751 (pm20) REVERT: D 272 ASN cc_start: 0.8242 (m-40) cc_final: 0.8006 (t0) REVERT: D 421 TRP cc_start: 0.6956 (t-100) cc_final: 0.6740 (t-100) REVERT: D 525 ASP cc_start: 0.7785 (t0) cc_final: 0.7405 (t70) REVERT: D 606 ARG cc_start: 0.7916 (ttm110) cc_final: 0.7412 (ttm110) REVERT: A 146 ASN cc_start: 0.8004 (t0) cc_final: 0.7446 (t0) REVERT: A 182 GLU cc_start: 0.8314 (pm20) cc_final: 0.7754 (pm20) REVERT: A 272 ASN cc_start: 0.8242 (m-40) cc_final: 0.8005 (t0) REVERT: A 525 ASP cc_start: 0.7793 (t0) cc_final: 0.7378 (t70) REVERT: B 146 ASN cc_start: 0.8156 (t0) cc_final: 0.7520 (t0) REVERT: B 272 ASN cc_start: 0.8289 (t0) cc_final: 0.8048 (t0) REVERT: B 507 LEU cc_start: 0.8237 (mm) cc_final: 0.8026 (mm) REVERT: B 525 ASP cc_start: 0.7811 (t0) cc_final: 0.7445 (t70) REVERT: B 558 PHE cc_start: 0.6962 (t80) cc_final: 0.6688 (t80) REVERT: C 146 ASN cc_start: 0.8016 (t0) cc_final: 0.7448 (t0) REVERT: C 182 GLU cc_start: 0.8297 (pm20) cc_final: 0.7744 (pm20) REVERT: C 272 ASN cc_start: 0.8328 (t0) cc_final: 0.8114 (t0) REVERT: C 525 ASP cc_start: 0.7822 (t0) cc_final: 0.7460 (t70) REVERT: C 558 PHE cc_start: 0.6884 (t80) cc_final: 0.6597 (t80) REVERT: C 606 ARG cc_start: 0.8171 (ttm110) cc_final: 0.7626 (ttm110) outliers start: 44 outliers final: 26 residues processed: 280 average time/residue: 0.3122 time to fit residues: 131.1884 Evaluate side-chains 260 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 234 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 578 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 458 ASN A 458 ASN B 458 ASN B 510 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 17756 Z= 0.364 Angle : 0.598 9.311 24036 Z= 0.305 Chirality : 0.042 0.163 2624 Planarity : 0.004 0.036 2948 Dihedral : 13.609 174.730 2564 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.22 % Allowed : 17.60 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.18), residues: 2040 helix: 0.71 (0.15), residues: 1152 sheet: -1.09 (0.39), residues: 104 loop : -1.97 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 421 HIS 0.004 0.001 HIS C 484 PHE 0.019 0.002 PHE C 159 TYR 0.019 0.001 TYR A 363 ARG 0.005 0.000 ARG B 535 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 234 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 146 ASN cc_start: 0.8173 (t0) cc_final: 0.7611 (t0) REVERT: D 272 ASN cc_start: 0.8255 (m-40) cc_final: 0.8000 (t0) REVERT: D 525 ASP cc_start: 0.7863 (t0) cc_final: 0.7461 (t70) REVERT: D 606 ARG cc_start: 0.7937 (ttm110) cc_final: 0.7378 (ttm110) REVERT: A 146 ASN cc_start: 0.8175 (t0) cc_final: 0.7614 (t0) REVERT: A 182 GLU cc_start: 0.8374 (pm20) cc_final: 0.7770 (pm20) REVERT: A 272 ASN cc_start: 0.8257 (m-40) cc_final: 0.7997 (t0) REVERT: A 525 ASP cc_start: 0.7808 (t0) cc_final: 0.7398 (t70) REVERT: A 558 PHE cc_start: 0.7103 (t80) cc_final: 0.6701 (t80) REVERT: A 606 ARG cc_start: 0.8013 (ttm110) cc_final: 0.7419 (ttm110) REVERT: B 146 ASN cc_start: 0.8242 (t0) cc_final: 0.7623 (t0) REVERT: B 507 LEU cc_start: 0.8170 (mm) cc_final: 0.7965 (mm) REVERT: B 525 ASP cc_start: 0.7864 (t0) cc_final: 0.7469 (t70) REVERT: B 558 PHE cc_start: 0.7096 (t80) cc_final: 0.6821 (t80) REVERT: B 606 ARG cc_start: 0.7993 (ttm110) cc_final: 0.7435 (ttm110) REVERT: C 146 ASN cc_start: 0.8180 (t0) cc_final: 0.7616 (t0) REVERT: C 182 GLU cc_start: 0.8385 (pm20) cc_final: 0.7959 (pm20) REVERT: C 272 ASN cc_start: 0.8497 (t0) cc_final: 0.8289 (t0) REVERT: C 421 TRP cc_start: 0.6767 (t-100) cc_final: 0.6414 (t-100) REVERT: C 525 ASP cc_start: 0.7849 (t0) cc_final: 0.7460 (t70) REVERT: C 558 PHE cc_start: 0.7130 (t80) cc_final: 0.6832 (t80) REVERT: C 606 ARG cc_start: 0.8078 (ttm110) cc_final: 0.7470 (ttm110) outliers start: 60 outliers final: 45 residues processed: 277 average time/residue: 0.3033 time to fit residues: 124.9928 Evaluate side-chains 276 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 231 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 458 ASN A 458 ASN B 458 ASN B 510 GLN C 458 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17756 Z= 0.217 Angle : 0.512 8.129 24036 Z= 0.263 Chirality : 0.039 0.149 2624 Planarity : 0.003 0.038 2948 Dihedral : 13.167 174.523 2564 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.52 % Allowed : 18.99 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 2040 helix: 0.91 (0.15), residues: 1172 sheet: -1.15 (0.37), residues: 128 loop : -1.70 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 421 HIS 0.002 0.001 HIS D 484 PHE 0.020 0.001 PHE B 159 TYR 0.013 0.001 TYR A 363 ARG 0.004 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 232 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 146 ASN cc_start: 0.8016 (t0) cc_final: 0.7457 (t0) REVERT: D 225 MET cc_start: 0.8131 (tpt) cc_final: 0.7301 (tpt) REVERT: D 272 ASN cc_start: 0.8251 (m-40) cc_final: 0.8017 (t0) REVERT: D 525 ASP cc_start: 0.7807 (t0) cc_final: 0.7434 (t70) REVERT: D 606 ARG cc_start: 0.7902 (ttm110) cc_final: 0.7443 (ttm110) REVERT: A 146 ASN cc_start: 0.8019 (t0) cc_final: 0.7459 (t0) REVERT: A 225 MET cc_start: 0.8131 (tpt) cc_final: 0.7295 (tpt) REVERT: A 272 ASN cc_start: 0.8247 (m-40) cc_final: 0.8008 (t0) REVERT: A 525 ASP cc_start: 0.7731 (t0) cc_final: 0.7332 (t70) REVERT: A 558 PHE cc_start: 0.7041 (t80) cc_final: 0.6637 (t80) REVERT: A 606 ARG cc_start: 0.7994 (ttm110) cc_final: 0.7394 (ttm110) REVERT: B 146 ASN cc_start: 0.8091 (t0) cc_final: 0.7444 (t0) REVERT: B 525 ASP cc_start: 0.7808 (t0) cc_final: 0.7445 (t70) REVERT: B 558 PHE cc_start: 0.7025 (t80) cc_final: 0.6748 (t80) REVERT: B 606 ARG cc_start: 0.7971 (ttm110) cc_final: 0.7413 (ttm110) REVERT: C 146 ASN cc_start: 0.8019 (t0) cc_final: 0.7453 (t0) REVERT: C 182 GLU cc_start: 0.8364 (pm20) cc_final: 0.7909 (pm20) REVERT: C 225 MET cc_start: 0.8146 (tpt) cc_final: 0.7310 (tpt) REVERT: C 272 ASN cc_start: 0.8454 (t0) cc_final: 0.8240 (t0) REVERT: C 421 TRP cc_start: 0.6760 (t-100) cc_final: 0.6372 (t-100) REVERT: C 525 ASP cc_start: 0.7845 (t0) cc_final: 0.7485 (t70) REVERT: C 558 PHE cc_start: 0.7063 (t80) cc_final: 0.6764 (t80) REVERT: C 606 ARG cc_start: 0.8054 (ttm110) cc_final: 0.7431 (ttm110) REVERT: C 608 LEU cc_start: 0.7675 (mt) cc_final: 0.7205 (pp) outliers start: 47 outliers final: 43 residues processed: 272 average time/residue: 0.3114 time to fit residues: 128.0433 Evaluate side-chains 267 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 224 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 2.9990 chunk 22 optimal weight: 0.0970 chunk 112 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 196 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 119 optimal weight: 0.1980 chunk 90 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17756 Z= 0.155 Angle : 0.483 7.473 24036 Z= 0.246 Chirality : 0.038 0.138 2624 Planarity : 0.003 0.038 2948 Dihedral : 12.716 171.862 2564 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.63 % Allowed : 18.94 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.19), residues: 2040 helix: 1.33 (0.16), residues: 1148 sheet: -0.87 (0.36), residues: 128 loop : -1.60 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 421 HIS 0.003 0.001 HIS A 484 PHE 0.023 0.001 PHE D 159 TYR 0.009 0.001 TYR A 363 ARG 0.004 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 238 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 117 SER cc_start: 0.8218 (m) cc_final: 0.7837 (p) REVERT: D 146 ASN cc_start: 0.7848 (t0) cc_final: 0.7327 (t0) REVERT: D 272 ASN cc_start: 0.8216 (m-40) cc_final: 0.8011 (t0) REVERT: D 525 ASP cc_start: 0.7841 (t0) cc_final: 0.7493 (t70) REVERT: D 558 PHE cc_start: 0.7013 (t80) cc_final: 0.6634 (t80) REVERT: D 606 ARG cc_start: 0.7885 (ttm110) cc_final: 0.7403 (ttm110) REVERT: A 117 SER cc_start: 0.8255 (m) cc_final: 0.7864 (p) REVERT: A 146 ASN cc_start: 0.7852 (t0) cc_final: 0.7318 (t0) REVERT: A 182 GLU cc_start: 0.8312 (pm20) cc_final: 0.7863 (pm20) REVERT: A 272 ASN cc_start: 0.8214 (m-40) cc_final: 0.8005 (t0) REVERT: A 525 ASP cc_start: 0.7814 (t0) cc_final: 0.7454 (t70) REVERT: A 558 PHE cc_start: 0.6972 (t80) cc_final: 0.6598 (t80) REVERT: B 117 SER cc_start: 0.8239 (m) cc_final: 0.7846 (p) REVERT: B 146 ASN cc_start: 0.7986 (t0) cc_final: 0.7353 (t0) REVERT: B 505 LEU cc_start: 0.8404 (tp) cc_final: 0.7968 (mp) REVERT: B 525 ASP cc_start: 0.7852 (t0) cc_final: 0.7516 (t70) REVERT: B 558 PHE cc_start: 0.6994 (t80) cc_final: 0.6732 (t80) REVERT: C 117 SER cc_start: 0.8240 (m) cc_final: 0.7857 (p) REVERT: C 146 ASN cc_start: 0.7857 (t0) cc_final: 0.7331 (t0) REVERT: C 182 GLU cc_start: 0.8308 (pm20) cc_final: 0.7852 (pm20) REVERT: C 525 ASP cc_start: 0.7837 (t0) cc_final: 0.7500 (t70) REVERT: C 558 PHE cc_start: 0.7052 (t80) cc_final: 0.6744 (t80) REVERT: C 608 LEU cc_start: 0.7721 (mt) cc_final: 0.7215 (pp) outliers start: 49 outliers final: 43 residues processed: 281 average time/residue: 0.3000 time to fit residues: 126.5171 Evaluate side-chains 271 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 228 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 125 optimal weight: 0.2980 chunk 133 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 18 optimal weight: 0.7980 chunk 154 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17756 Z= 0.188 Angle : 0.506 7.902 24036 Z= 0.256 Chirality : 0.038 0.142 2624 Planarity : 0.003 0.038 2948 Dihedral : 12.588 171.141 2564 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.79 % Allowed : 19.21 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 2040 helix: 1.31 (0.16), residues: 1172 sheet: -0.80 (0.36), residues: 128 loop : -1.49 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 421 HIS 0.008 0.001 HIS A 484 PHE 0.022 0.002 PHE B 159 TYR 0.012 0.001 TYR A 363 ARG 0.007 0.000 ARG D 535 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 228 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 117 SER cc_start: 0.8200 (m) cc_final: 0.7827 (p) REVERT: D 146 ASN cc_start: 0.7873 (t0) cc_final: 0.7340 (t0) REVERT: D 182 GLU cc_start: 0.8336 (pm20) cc_final: 0.7903 (pm20) REVERT: D 272 ASN cc_start: 0.8225 (m-40) cc_final: 0.8008 (t0) REVERT: D 505 LEU cc_start: 0.8401 (tp) cc_final: 0.7998 (mp) REVERT: D 525 ASP cc_start: 0.7857 (t0) cc_final: 0.7513 (t70) REVERT: D 558 PHE cc_start: 0.7036 (t80) cc_final: 0.6676 (t80) REVERT: A 117 SER cc_start: 0.8222 (m) cc_final: 0.7849 (p) REVERT: A 146 ASN cc_start: 0.7873 (t0) cc_final: 0.7344 (t0) REVERT: A 272 ASN cc_start: 0.8217 (m-40) cc_final: 0.8005 (t0) REVERT: A 525 ASP cc_start: 0.7831 (t0) cc_final: 0.7473 (t70) REVERT: A 558 PHE cc_start: 0.6953 (t80) cc_final: 0.6579 (t80) REVERT: B 117 SER cc_start: 0.8204 (m) cc_final: 0.7824 (p) REVERT: B 146 ASN cc_start: 0.8010 (t0) cc_final: 0.7364 (t0) REVERT: B 525 ASP cc_start: 0.7860 (t0) cc_final: 0.7525 (t70) REVERT: B 558 PHE cc_start: 0.6906 (t80) cc_final: 0.6638 (t80) REVERT: C 117 SER cc_start: 0.8221 (m) cc_final: 0.7839 (p) REVERT: C 146 ASN cc_start: 0.7874 (t0) cc_final: 0.7342 (t0) REVERT: C 182 GLU cc_start: 0.8306 (pm20) cc_final: 0.7880 (pm20) REVERT: C 525 ASP cc_start: 0.7853 (t0) cc_final: 0.7523 (t70) REVERT: C 558 PHE cc_start: 0.7037 (t80) cc_final: 0.6724 (t80) REVERT: C 608 LEU cc_start: 0.7720 (mt) cc_final: 0.7223 (pp) outliers start: 52 outliers final: 48 residues processed: 274 average time/residue: 0.2936 time to fit residues: 120.0381 Evaluate side-chains 275 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 227 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 617 LEU 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: 0.8980 chunk 183 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 165 optimal weight: 0.0970 chunk 173 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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: 0.8033 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17756 Z= 0.135 Angle : 0.482 6.989 24036 Z= 0.244 Chirality : 0.037 0.133 2624 Planarity : 0.003 0.039 2948 Dihedral : 12.146 167.203 2564 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.41 % Allowed : 19.53 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.19), residues: 2040 helix: 1.49 (0.16), residues: 1180 sheet: -0.47 (0.38), residues: 116 loop : -1.46 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 421 HIS 0.005 0.001 HIS A 484 PHE 0.022 0.001 PHE B 159 TYR 0.008 0.001 TYR A 365 ARG 0.014 0.000 ARG C 606 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 226 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 146 ASN cc_start: 0.7727 (t0) cc_final: 0.7224 (t0) REVERT: D 525 ASP cc_start: 0.7887 (t0) cc_final: 0.7605 (t70) REVERT: D 558 PHE cc_start: 0.7007 (t80) cc_final: 0.6660 (t80) REVERT: A 117 SER cc_start: 0.8186 (m) cc_final: 0.7856 (p) REVERT: A 146 ASN cc_start: 0.7727 (t0) cc_final: 0.7229 (t0) REVERT: A 272 ASN cc_start: 0.8207 (m-40) cc_final: 0.8006 (t0) REVERT: A 525 ASP cc_start: 0.7823 (t0) cc_final: 0.7504 (t70) REVERT: A 558 PHE cc_start: 0.6892 (t80) cc_final: 0.6535 (t80) REVERT: A 606 ARG cc_start: 0.8317 (ttm110) cc_final: 0.7969 (ttm110) REVERT: B 146 ASN cc_start: 0.7874 (t0) cc_final: 0.7261 (t0) REVERT: B 525 ASP cc_start: 0.7866 (t0) cc_final: 0.7568 (t70) REVERT: B 558 PHE cc_start: 0.6892 (t80) cc_final: 0.6649 (t80) REVERT: C 117 SER cc_start: 0.8177 (m) cc_final: 0.7851 (p) REVERT: C 146 ASN cc_start: 0.7729 (t0) cc_final: 0.7227 (t0) REVERT: C 182 GLU cc_start: 0.8288 (pm20) cc_final: 0.7847 (pm20) REVERT: C 525 ASP cc_start: 0.7866 (t0) cc_final: 0.7582 (t70) REVERT: C 558 PHE cc_start: 0.6900 (t80) cc_final: 0.6596 (t80) REVERT: C 606 ARG cc_start: 0.8111 (ttm110) cc_final: 0.7797 (ttm110) REVERT: C 608 LEU cc_start: 0.7785 (mt) cc_final: 0.7275 (pp) outliers start: 45 outliers final: 45 residues processed: 268 average time/residue: 0.3163 time to fit residues: 127.0858 Evaluate side-chains 258 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 213 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 125 optimal weight: 0.0070 chunk 99 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17756 Z= 0.258 Angle : 0.550 8.432 24036 Z= 0.279 Chirality : 0.040 0.150 2624 Planarity : 0.004 0.046 2948 Dihedral : 12.391 169.261 2564 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.63 % Allowed : 19.58 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.19), residues: 2040 helix: 1.35 (0.15), residues: 1180 sheet: -0.45 (0.40), residues: 116 loop : -1.49 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 421 HIS 0.006 0.001 HIS A 484 PHE 0.022 0.002 PHE C 159 TYR 0.016 0.001 TYR A 363 ARG 0.014 0.000 ARG B 606 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 227 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 117 SER cc_start: 0.8201 (m) cc_final: 0.7820 (p) REVERT: D 146 ASN cc_start: 0.7891 (t0) cc_final: 0.7382 (t0) REVERT: D 525 ASP cc_start: 0.7898 (t0) cc_final: 0.7584 (t70) REVERT: D 558 PHE cc_start: 0.7108 (t80) cc_final: 0.6781 (t80) REVERT: D 606 ARG cc_start: 0.8084 (ttm110) cc_final: 0.7717 (ttm110) REVERT: A 117 SER cc_start: 0.8247 (m) cc_final: 0.7876 (p) REVERT: A 146 ASN cc_start: 0.7895 (t0) cc_final: 0.7386 (t0) REVERT: A 525 ASP cc_start: 0.7879 (t0) cc_final: 0.7536 (t70) REVERT: A 558 PHE cc_start: 0.6934 (t80) cc_final: 0.6571 (t80) REVERT: B 117 SER cc_start: 0.8203 (m) cc_final: 0.7819 (p) REVERT: B 146 ASN cc_start: 0.7978 (t0) cc_final: 0.7365 (t0) REVERT: B 525 ASP cc_start: 0.7885 (t0) cc_final: 0.7572 (t70) REVERT: B 558 PHE cc_start: 0.6905 (t80) cc_final: 0.6641 (t80) REVERT: C 117 SER cc_start: 0.8238 (m) cc_final: 0.7855 (p) REVERT: C 146 ASN cc_start: 0.7898 (t0) cc_final: 0.7387 (t0) REVERT: C 182 GLU cc_start: 0.8359 (pm20) cc_final: 0.7915 (pm20) REVERT: C 525 ASP cc_start: 0.7887 (t0) cc_final: 0.7583 (t70) REVERT: C 558 PHE cc_start: 0.7005 (t80) cc_final: 0.6686 (t80) REVERT: C 608 LEU cc_start: 0.7731 (mt) cc_final: 0.7213 (pp) outliers start: 49 outliers final: 44 residues processed: 265 average time/residue: 0.3070 time to fit residues: 121.5994 Evaluate side-chains 269 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 225 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 162 optimal weight: 0.9990 chunk 67 optimal weight: 0.0980 chunk 166 optimal weight: 0.1980 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 425 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.171720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119968 restraints weight = 22645.047| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.21 r_work: 0.3317 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17756 Z= 0.131 Angle : 0.488 6.639 24036 Z= 0.248 Chirality : 0.037 0.133 2624 Planarity : 0.003 0.048 2948 Dihedral : 11.922 165.099 2564 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.15 % Allowed : 20.17 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 2040 helix: 1.52 (0.15), residues: 1204 sheet: -0.05 (0.41), residues: 116 loop : -1.43 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 421 HIS 0.005 0.001 HIS A 484 PHE 0.022 0.001 PHE A 159 TYR 0.011 0.001 TYR B 244 ARG 0.014 0.000 ARG C 606 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3905.41 seconds wall clock time: 71 minutes 43.29 seconds (4303.29 seconds total)