Starting phenix.real_space_refine on Sun Mar 17 17:42:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj3_33218/03_2024/7xj3_33218_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj3_33218/03_2024/7xj3_33218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj3_33218/03_2024/7xj3_33218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj3_33218/03_2024/7xj3_33218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj3_33218/03_2024/7xj3_33218_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj3_33218/03_2024/7xj3_33218_updated.pdb" } resolution = 3.54 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= 0.004 sd= 0.113 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12225 2.51 5 N 3047 2.21 5 O 3109 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ASP 240": "OD1" <-> "OD2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ASP 379": "OD1" <-> "OD2" Residue "B TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 396": "OD1" <-> "OD2" Residue "B PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B GLU 501": "OE1" <-> "OE2" Residue "B PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "B GLU 751": "OE1" <-> "OE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C ASP 293": "OD1" <-> "OD2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C GLU 364": "OE1" <-> "OE2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ASP 379": "OD1" <-> "OD2" Residue "C TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 396": "OD1" <-> "OD2" Residue "C PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C GLU 501": "OE1" <-> "OE2" Residue "C PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 610": "OE1" <-> "OE2" Residue "C TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 156": "OD1" <-> "OD2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ASP 240": "OD1" <-> "OD2" Residue "D ASP 293": "OD1" <-> "OD2" Residue "D GLU 308": "OE1" <-> "OE2" Residue "D ARG 319": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ASP 379": "OD1" <-> "OD2" Residue "D TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 396": "OD1" <-> "OD2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D GLU 501": "OE1" <-> "OE2" Residue "D PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D ASP 586": "OD1" <-> "OD2" Residue "D TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 610": "OE1" <-> "OE2" Residue "D TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18493 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4590 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 13, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 359 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 293 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 26, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 244 Chain: "C" Number of atoms: 4580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4580 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 13, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 27, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 254 Chain: "A" Number of atoms: 4576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4576 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 13, 'TRANS': 593} Chain breaks: 4 Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 27, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 254 Chain: "D" Number of atoms: 4576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4576 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 13, 'TRANS': 593} Chain breaks: 4 Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 27, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 254 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'6OU': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'6OU:plan-2': 3, '6OU:plan-3': 3} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {'6OU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'6OU:plan-2': 4, '6OU:plan-3': 4} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {'6OU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'6OU:plan-2': 4, '6OU:plan-3': 4} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'6OU': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'6OU:plan-1': 1, '6OU:plan-2': 3, '6OU:plan-3': 3} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 9.54, per 1000 atoms: 0.52 Number of scatterers: 18493 At special positions: 0 Unit cell: (142.79, 144.97, 126.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3109 8.00 N 3047 7.00 C 12225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 7.27 Conformation dependent library (CDL) restraints added in 3.9 seconds 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 4 sheets defined 57.0% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'B' and resid 120 through 129 Processing helix chain 'B' and resid 133 through 147 Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.707A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 229 through 237 removed outlier: 3.508A pdb=" N ALA B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 299 through 306 Processing helix chain 'B' and resid 317 through 326 Processing helix chain 'B' and resid 344 through 350 Processing helix chain 'B' and resid 354 through 361 removed outlier: 3.597A pdb=" N LYS B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 423 through 460 removed outlier: 4.144A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LYS B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N HIS B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 507 removed outlier: 3.836A pdb=" N PHE B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LEU B 507 " --> pdb=" O ILE B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 541 Processing helix chain 'B' and resid 547 through 567 removed outlier: 5.122A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 585 Processing helix chain 'B' and resid 587 through 608 Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'B' and resid 625 through 637 Processing helix chain 'B' and resid 651 through 666 Processing helix chain 'B' and resid 669 through 705 removed outlier: 3.674A pdb=" N GLU B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU B 687 " --> pdb=" O ASN B 683 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ARG B 690 " --> pdb=" O LYS B 686 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 715 Processing helix chain 'C' and resid 120 through 129 Processing helix chain 'C' and resid 133 through 147 Processing helix chain 'C' and resid 155 through 162 Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.713A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 229 through 237 removed outlier: 3.507A pdb=" N ALA C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 Processing helix chain 'C' and resid 275 through 282 Processing helix chain 'C' and resid 299 through 306 Processing helix chain 'C' and resid 317 through 326 Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 354 through 361 removed outlier: 3.608A pdb=" N LYS C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 423 through 460 removed outlier: 4.148A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LYS C 438 " --> pdb=" O LYS C 434 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N HIS C 439 " --> pdb=" O LYS C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 506 removed outlier: 3.823A pdb=" N PHE C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 541 Processing helix chain 'C' and resid 547 through 567 removed outlier: 5.121A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG C 567 " --> pdb=" O LEU C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 585 Processing helix chain 'C' and resid 587 through 608 Processing helix chain 'C' and resid 617 through 619 No H-bonds generated for 'chain 'C' and resid 617 through 619' Processing helix chain 'C' and resid 625 through 637 Processing helix chain 'C' and resid 651 through 666 Processing helix chain 'C' and resid 669 through 705 removed outlier: 3.628A pdb=" N GLU C 682 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLU C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ARG C 690 " --> pdb=" O LYS C 686 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 715 Processing helix chain 'A' and resid 120 through 129 Processing helix chain 'A' and resid 133 through 147 Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.708A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.513A pdb=" N ALA A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 299 through 306 Processing helix chain 'A' and resid 317 through 326 Processing helix chain 'A' and resid 344 through 350 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 423 through 460 removed outlier: 4.142A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N HIS A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 505 Processing helix chain 'A' and resid 522 through 541 Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.540A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 585 Processing helix chain 'A' and resid 587 through 608 Processing helix chain 'A' and resid 625 through 637 Processing helix chain 'A' and resid 651 through 666 Processing helix chain 'A' and resid 669 through 705 removed outlier: 3.630A pdb=" N GLU A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLU A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ARG A 690 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 715 Processing helix chain 'D' and resid 120 through 129 Processing helix chain 'D' and resid 133 through 147 Processing helix chain 'D' and resid 155 through 162 Processing helix chain 'D' and resid 171 through 176 Processing helix chain 'D' and resid 183 through 196 removed outlier: 3.713A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 229 through 236 Processing helix chain 'D' and resid 265 through 271 Processing helix chain 'D' and resid 275 through 282 Processing helix chain 'D' and resid 299 through 306 Processing helix chain 'D' and resid 317 through 326 Processing helix chain 'D' and resid 344 through 350 Processing helix chain 'D' and resid 355 through 361 Processing helix chain 'D' and resid 371 through 373 No H-bonds generated for 'chain 'D' and resid 371 through 373' Processing helix chain 'D' and resid 403 through 409 Processing helix chain 'D' and resid 423 through 460 removed outlier: 4.145A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LYS D 438 " --> pdb=" O LYS D 434 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N HIS D 439 " --> pdb=" O LYS D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 507 removed outlier: 3.832A pdb=" N PHE D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU D 507 " --> pdb=" O ILE D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 541 Processing helix chain 'D' and resid 547 through 561 Processing helix chain 'D' and resid 565 through 567 No H-bonds generated for 'chain 'D' and resid 565 through 567' Processing helix chain 'D' and resid 570 through 585 Processing helix chain 'D' and resid 587 through 608 Processing helix chain 'D' and resid 625 through 637 Processing helix chain 'D' and resid 651 through 666 Processing helix chain 'D' and resid 669 through 705 removed outlier: 3.628A pdb=" N GLU D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLU D 687 " --> pdb=" O ASN D 683 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ARG D 690 " --> pdb=" O LYS D 686 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 715 Processing sheet with id= A, first strand: chain 'B' and resid 376 through 378 removed outlier: 3.862A pdb=" N ARG B 729 " --> pdb=" O CYS B 721 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 376 through 378 removed outlier: 3.827A pdb=" N ARG C 729 " --> pdb=" O CYS C 721 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 376 through 378 removed outlier: 3.845A pdb=" N ARG A 729 " --> pdb=" O CYS A 721 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 376 through 378 removed outlier: 3.865A pdb=" N ARG D 729 " --> pdb=" O CYS D 721 " (cutoff:3.500A) 940 hydrogen bonds defined for protein. 2802 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: 5.29 Time building geometry restraints manager: 7.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.55: 18680 1.55 - 1.91: 191 1.91 - 2.27: 0 2.27 - 2.64: 0 2.64 - 3.00: 2 Bond restraints: 18873 Sorted by residual: bond pdb=" C PRO C 613 " pdb=" N ASN C 616 " ideal model delta sigma weight residual 1.332 2.998 -1.666 1.40e-02 5.10e+03 1.42e+04 bond pdb=" C PRO B 613 " pdb=" N ASN B 616 " ideal model delta sigma weight residual 1.332 2.997 -1.664 1.40e-02 5.10e+03 1.41e+04 bond pdb=" C PRO B 753 " pdb=" O PRO B 753 " ideal model delta sigma weight residual 1.233 1.186 0.047 1.10e-02 8.26e+03 1.86e+01 bond pdb=" C PRO A 753 " pdb=" O PRO A 753 " ideal model delta sigma weight residual 1.233 1.184 0.049 1.16e-02 7.43e+03 1.75e+01 bond pdb=" C PRO D 753 " pdb=" O PRO D 753 " ideal model delta sigma weight residual 1.233 1.185 0.048 1.16e-02 7.43e+03 1.72e+01 ... (remaining 18868 not shown) Histogram of bond angle deviations from ideal: 68.63 - 84.60: 2 84.60 - 100.57: 39 100.57 - 116.53: 12496 116.53 - 132.50: 13033 132.50 - 148.46: 44 Bond angle restraints: 25614 Sorted by residual: angle pdb=" O PRO B 613 " pdb=" C PRO B 613 " pdb=" N ASN B 616 " ideal model delta sigma weight residual 122.64 68.63 54.01 1.35e+00 5.49e-01 1.60e+03 angle pdb=" O PRO C 613 " pdb=" C PRO C 613 " pdb=" N ASN C 616 " ideal model delta sigma weight residual 122.64 68.83 53.81 1.35e+00 5.49e-01 1.59e+03 angle pdb=" C PRO B 613 " pdb=" N ASN B 616 " pdb=" CA ASN B 616 " ideal model delta sigma weight residual 121.54 148.46 -26.92 1.91e+00 2.74e-01 1.99e+02 angle pdb=" C PRO C 613 " pdb=" N ASN C 616 " pdb=" CA ASN C 616 " ideal model delta sigma weight residual 121.54 148.43 -26.89 1.91e+00 2.74e-01 1.98e+02 angle pdb=" CA PRO B 613 " pdb=" C PRO B 613 " pdb=" N ASN B 616 " ideal model delta sigma weight residual 116.70 142.75 -26.05 2.07e+00 2.33e-01 1.58e+02 ... (remaining 25609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 10132 24.23 - 48.45: 829 48.45 - 72.68: 73 72.68 - 96.90: 12 96.90 - 121.13: 3 Dihedral angle restraints: 11049 sinusoidal: 3919 harmonic: 7130 Sorted by residual: dihedral pdb=" CA PRO B 613 " pdb=" C PRO B 613 " pdb=" N ASN B 616 " pdb=" CA ASN B 616 " ideal model delta harmonic sigma weight residual -180.00 -65.76 -114.24 0 5.00e+00 4.00e-02 5.22e+02 dihedral pdb=" CA PRO C 613 " pdb=" C PRO C 613 " pdb=" N ASN C 616 " pdb=" CA ASN C 616 " ideal model delta harmonic sigma weight residual -180.00 -66.03 -113.97 0 5.00e+00 4.00e-02 5.20e+02 dihedral pdb=" CA HIS A 585 " pdb=" C HIS A 585 " pdb=" N ASP A 586 " pdb=" CA ASP A 586 " ideal model delta harmonic sigma weight residual -180.00 -159.85 -20.15 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 11046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1878 0.036 - 0.072: 901 0.072 - 0.108: 210 0.108 - 0.143: 65 0.143 - 0.179: 6 Chirality restraints: 3060 Sorted by residual: chirality pdb=" CA ILE D 609 " pdb=" N ILE D 609 " pdb=" C ILE D 609 " pdb=" CB ILE D 609 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.04e-01 chirality pdb=" CA ILE A 609 " pdb=" N ILE A 609 " pdb=" C ILE A 609 " pdb=" CB ILE A 609 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CA GLU A 423 " pdb=" N GLU A 423 " pdb=" C GLU A 423 " pdb=" CB GLU A 423 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.74e-01 ... (remaining 3057 not shown) Planarity restraints: 3146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO C 613 " -0.169 2.00e-02 2.50e+03 1.94e-01 3.78e+02 pdb=" C PRO C 613 " 0.330 2.00e-02 2.50e+03 pdb=" O PRO C 613 " -0.101 2.00e-02 2.50e+03 pdb=" N ASN C 616 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 613 " -0.169 2.00e-02 2.50e+03 1.94e-01 3.76e+02 pdb=" C PRO B 613 " 0.329 2.00e-02 2.50e+03 pdb=" O PRO B 613 " -0.100 2.00e-02 2.50e+03 pdb=" N ASN B 616 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 352 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C GLY A 352 " 0.032 2.00e-02 2.50e+03 pdb=" O GLY A 352 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS A 353 " -0.011 2.00e-02 2.50e+03 ... (remaining 3143 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4479 2.77 - 3.31: 17112 3.31 - 3.84: 28513 3.84 - 4.37: 31100 4.37 - 4.90: 57056 Nonbonded interactions: 138260 Sorted by model distance: nonbonded pdb=" N ASN D 178 " pdb=" OD1 ASN D 178 " model vdw 2.242 2.520 nonbonded pdb=" N ASN A 178 " pdb=" OD1 ASN A 178 " model vdw 2.243 2.520 nonbonded pdb=" N ASN B 178 " pdb=" OD1 ASN B 178 " model vdw 2.248 2.520 nonbonded pdb=" CE1 TYR D 622 " pdb=" OE1 GLU D 631 " model vdw 2.251 3.340 nonbonded pdb=" OH TYR C 260 " pdb=" ND2 ASN C 297 " model vdw 2.256 2.520 ... (remaining 138255 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 118 through 754 or (resid 1401 and (name C36 or name C37 o \ r name C38 or name C39 or name C40 or name C41 or name C42 or name C43)) or resi \ d 1403)) selection = (chain 'B' and (resid 118 through 610 or (resid 611 and (name N or name CA or na \ me C or name O or name CB )) or resid 612 through 749 or (resid 750 through 752 \ and (name N or name CA or name C or name O or name CB )) or resid 753 through 75 \ 4 or (resid 1501 and (name C36 or name C37 or name C38 or name C39 or name C40 o \ r name C41 or name C42 or name C43)) or (resid 1503 and (name C38 or name C39 or \ name C40 or name C41 or name C42 or name C43 or name C44 or name C45 or name C4 \ 6 or name C47 or name C48 or name C49)))) selection = (chain 'C' and (resid 118 through 610 or (resid 611 and (name N or name CA or na \ me C or name O or name CB )) or resid 612 through 754 or resid 1701 or (resid 17 \ 03 and (name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or \ name C44 or name C45 or name C46 or name C47 or name C48 or name C49)))) selection = (chain 'D' and (resid 118 through 754 or (resid 1701 and (name C36 or name C37 o \ r name C38 or name C39 or name C40 or name C41 or name C42 or name C43)) or (res \ id 1703 and (name C38 or name C39 or name C40 or name C41 or name C42 or name C4 \ 3 or name C44 or name C45 or name C46 or name C47 or name C48 or name C49)))) } 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 group one per residue 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: 1.510 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: 0.030 Extract box with map and model: 4.530 Check model and map are aligned: 0.310 Set scattering table: 0.160 Process input model: 48.160 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.019 1.666 18873 Z= 1.225 Angle : 1.030 54.007 25614 Z= 0.611 Chirality : 0.043 0.179 3060 Planarity : 0.006 0.194 3146 Dihedral : 16.434 121.126 6417 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.79 % Favored : 91.16 % Rotamer: Outliers : 6.79 % Allowed : 21.13 % Favored : 72.08 % 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: -3.52 (0.14), residues: 2388 helix: -1.44 (0.11), residues: 1536 sheet: -3.89 (0.50), residues: 56 loop : -3.90 (0.16), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 380 HIS 0.011 0.001 HIS C 301 PHE 0.017 0.002 PHE C 625 TYR 0.023 0.002 TYR B 451 ARG 0.004 0.000 ARG D 690 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 266 time to evaluate : 1.886 Fit side-chains REVERT: B 205 ASN cc_start: 0.9032 (t0) cc_final: 0.8818 (t0) REVERT: B 572 MET cc_start: 0.7875 (tpt) cc_final: 0.7545 (mmt) REVERT: B 586 ASP cc_start: 0.6808 (m-30) cc_final: 0.6059 (m-30) REVERT: B 652 ILE cc_start: 0.8473 (mp) cc_final: 0.8197 (mm) REVERT: C 299 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8494 (tp) REVERT: C 358 LYS cc_start: 0.9251 (tttm) cc_final: 0.8925 (tttp) REVERT: C 396 ASP cc_start: 0.8333 (t70) cc_final: 0.8065 (t70) REVERT: C 488 MET cc_start: 0.8126 (mtm) cc_final: 0.7903 (mpp) REVERT: C 572 MET cc_start: 0.7856 (tpt) cc_final: 0.7531 (mmp) REVERT: C 586 ASP cc_start: 0.6788 (m-30) cc_final: 0.6028 (m-30) REVERT: C 652 ILE cc_start: 0.8445 (mp) cc_final: 0.8202 (mm) REVERT: A 205 ASN cc_start: 0.9033 (t0) cc_final: 0.8824 (t0) REVERT: A 320 MET cc_start: 0.8624 (mmm) cc_final: 0.8197 (mmm) REVERT: A 396 ASP cc_start: 0.8337 (t70) cc_final: 0.8073 (t70) REVERT: A 442 PHE cc_start: 0.7130 (t80) cc_final: 0.6526 (m-10) REVERT: A 562 MET cc_start: 0.8685 (mmm) cc_final: 0.8415 (mmt) REVERT: A 572 MET cc_start: 0.7874 (tpt) cc_final: 0.7568 (mmt) REVERT: A 574 MET cc_start: 0.7635 (mtt) cc_final: 0.7277 (mtt) REVERT: A 586 ASP cc_start: 0.6793 (m-30) cc_final: 0.6059 (m-30) REVERT: A 652 ILE cc_start: 0.8405 (mp) cc_final: 0.8160 (mm) REVERT: D 234 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8340 (mp) REVERT: D 320 MET cc_start: 0.8624 (mmm) cc_final: 0.8167 (mmm) REVERT: D 396 ASP cc_start: 0.8306 (t70) cc_final: 0.8037 (t70) REVERT: D 442 PHE cc_start: 0.7120 (t80) cc_final: 0.6558 (m-10) REVERT: D 572 MET cc_start: 0.7848 (tpt) cc_final: 0.7545 (mmt) REVERT: D 586 ASP cc_start: 0.6794 (m-30) cc_final: 0.6061 (m-30) outliers start: 118 outliers final: 96 residues processed: 368 average time/residue: 0.2589 time to fit residues: 150.5538 Evaluate side-chains 322 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 224 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 284 HIS Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 521 TRP Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 405 GLU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 521 TRP Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 622 TYR Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN B 301 HIS B 346 GLN B 410 ASN B 585 HIS B 695 GLN C 297 ASN C 301 HIS C 346 GLN C 410 ASN C 452 ASN C 585 HIS A 297 ASN A 301 HIS A 346 GLN A 410 ASN A 585 HIS D 297 ASN D 301 HIS D 346 GLN D 410 ASN D 585 HIS D 646 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18873 Z= 0.290 Angle : 0.552 5.664 25614 Z= 0.292 Chirality : 0.038 0.140 3060 Planarity : 0.003 0.030 3146 Dihedral : 9.037 128.855 2873 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.65 % Favored : 93.31 % Rotamer: Outliers : 4.38 % Allowed : 24.12 % Favored : 71.50 % 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: -1.94 (0.16), residues: 2392 helix: -0.11 (0.13), residues: 1532 sheet: -3.13 (0.52), residues: 52 loop : -3.52 (0.16), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 380 HIS 0.008 0.001 HIS A 301 PHE 0.017 0.001 PHE B 489 TYR 0.016 0.001 TYR D 451 ARG 0.003 0.000 ARG B 462 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 235 time to evaluate : 1.994 Fit side-chains REVERT: B 205 ASN cc_start: 0.8986 (t0) cc_final: 0.8784 (t0) REVERT: B 487 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.5242 (mmm160) REVERT: B 488 MET cc_start: 0.8132 (mpp) cc_final: 0.7778 (mpp) REVERT: B 572 MET cc_start: 0.7755 (tpt) cc_final: 0.7345 (mmt) REVERT: B 586 ASP cc_start: 0.6899 (m-30) cc_final: 0.6477 (m-30) REVERT: C 358 LYS cc_start: 0.9187 (tttm) cc_final: 0.8968 (tttp) REVERT: C 488 MET cc_start: 0.8056 (mtm) cc_final: 0.7804 (mpp) REVERT: C 572 MET cc_start: 0.7714 (tpt) cc_final: 0.7304 (mmt) REVERT: C 574 MET cc_start: 0.7593 (mtt) cc_final: 0.7216 (mtt) REVERT: C 586 ASP cc_start: 0.6977 (m-30) cc_final: 0.6601 (m-30) REVERT: A 205 ASN cc_start: 0.8993 (t0) cc_final: 0.8788 (t0) REVERT: A 488 MET cc_start: 0.8191 (mpp) cc_final: 0.7942 (mpp) REVERT: A 572 MET cc_start: 0.7784 (tpt) cc_final: 0.7415 (mmt) REVERT: A 586 ASP cc_start: 0.6998 (m-30) cc_final: 0.6668 (m-30) REVERT: D 442 PHE cc_start: 0.7059 (t80) cc_final: 0.6419 (m-10) REVERT: D 488 MET cc_start: 0.8158 (mpp) cc_final: 0.7873 (mpp) REVERT: D 574 MET cc_start: 0.7477 (mtt) cc_final: 0.7132 (mtt) REVERT: D 586 ASP cc_start: 0.6993 (m-30) cc_final: 0.6599 (m-30) REVERT: D 645 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7325 (tm-30) REVERT: D 652 ILE cc_start: 0.8341 (mp) cc_final: 0.7984 (mm) REVERT: D 672 MET cc_start: 0.7096 (ttp) cc_final: 0.6887 (ttp) outliers start: 76 outliers final: 52 residues processed: 299 average time/residue: 0.2717 time to fit residues: 128.7329 Evaluate side-chains 283 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 230 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 521 TRP Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 521 TRP Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 679 GLU Chi-restraints excluded: chain D residue 681 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 0.7980 chunk 235 optimal weight: 0.7980 chunk 194 optimal weight: 0.7980 chunk 216 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 175 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 GLN B 410 ASN B 452 ASN C 313 GLN C 410 ASN A 297 ASN A 410 ASN D 297 ASN D 313 GLN D 410 ASN D 452 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18873 Z= 0.142 Angle : 0.454 5.580 25614 Z= 0.242 Chirality : 0.035 0.147 3060 Planarity : 0.003 0.033 3146 Dihedral : 6.911 111.815 2744 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.43 % Favored : 95.53 % Rotamer: Outliers : 3.91 % Allowed : 25.85 % Favored : 70.24 % 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: -0.91 (0.17), residues: 2392 helix: 0.67 (0.14), residues: 1552 sheet: -2.72 (0.50), residues: 52 loop : -3.13 (0.17), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 380 HIS 0.003 0.000 HIS A 301 PHE 0.012 0.001 PHE C 489 TYR 0.016 0.001 TYR C 451 ARG 0.003 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 264 time to evaluate : 1.866 Fit side-chains REVERT: B 205 ASN cc_start: 0.8907 (t0) cc_final: 0.8686 (t0) REVERT: B 234 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8418 (mp) REVERT: B 320 MET cc_start: 0.8352 (mmm) cc_final: 0.7596 (mmm) REVERT: B 488 MET cc_start: 0.8041 (mpp) cc_final: 0.7808 (mpp) REVERT: C 234 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8384 (mp) REVERT: C 320 MET cc_start: 0.8269 (mmm) cc_final: 0.7598 (mmm) REVERT: C 488 MET cc_start: 0.7965 (mtm) cc_final: 0.7726 (mpp) REVERT: A 234 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8377 (mp) REVERT: A 320 MET cc_start: 0.8345 (mmm) cc_final: 0.7623 (mmm) REVERT: A 488 MET cc_start: 0.8130 (mpp) cc_final: 0.7869 (mpp) REVERT: A 643 ASN cc_start: 0.6797 (OUTLIER) cc_final: 0.6226 (p0) REVERT: D 320 MET cc_start: 0.8346 (mmm) cc_final: 0.7721 (mmm) REVERT: D 488 MET cc_start: 0.8056 (mpp) cc_final: 0.7749 (mpp) REVERT: D 574 MET cc_start: 0.7473 (mtt) cc_final: 0.7051 (mtt) REVERT: D 645 GLN cc_start: 0.7478 (tm-30) cc_final: 0.7222 (tm-30) outliers start: 68 outliers final: 43 residues processed: 319 average time/residue: 0.2713 time to fit residues: 135.5095 Evaluate side-chains 270 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 223 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 521 TRP Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 284 HIS Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 521 TRP Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 207 optimal weight: 0.1980 chunk 62 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN B 452 ASN C 297 ASN A 452 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 18873 Z= 0.186 Angle : 0.479 6.976 25614 Z= 0.251 Chirality : 0.036 0.125 3060 Planarity : 0.003 0.033 3146 Dihedral : 6.678 107.221 2740 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.10 % Favored : 94.86 % Rotamer: Outliers : 4.95 % Allowed : 25.16 % Favored : 69.89 % 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: -0.56 (0.17), residues: 2392 helix: 0.96 (0.14), residues: 1544 sheet: -2.55 (0.48), residues: 52 loop : -2.99 (0.17), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 380 HIS 0.004 0.001 HIS D 301 PHE 0.010 0.001 PHE C 625 TYR 0.019 0.001 TYR D 451 ARG 0.004 0.000 ARG D 693 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 225 time to evaluate : 2.046 Fit side-chains REVERT: B 205 ASN cc_start: 0.8918 (t0) cc_final: 0.8678 (t0) REVERT: B 234 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8395 (mp) REVERT: B 320 MET cc_start: 0.8380 (mmm) cc_final: 0.7719 (mmm) REVERT: B 488 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7759 (mpp) REVERT: B 572 MET cc_start: 0.7437 (mmm) cc_final: 0.7177 (mmp) REVERT: C 234 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8374 (mp) REVERT: C 320 MET cc_start: 0.8293 (mmm) cc_final: 0.7708 (mmm) REVERT: C 643 ASN cc_start: 0.6644 (OUTLIER) cc_final: 0.6138 (p0) REVERT: A 234 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8353 (mp) REVERT: A 320 MET cc_start: 0.8366 (mmm) cc_final: 0.7732 (mmm) REVERT: A 488 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7824 (mpp) REVERT: A 647 ASN cc_start: 0.7970 (t0) cc_final: 0.7666 (t0) REVERT: D 234 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8292 (mp) REVERT: D 320 MET cc_start: 0.8375 (mmm) cc_final: 0.7712 (mmm) REVERT: D 358 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8743 (tttp) REVERT: D 488 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7759 (mpp) REVERT: D 652 ILE cc_start: 0.8321 (mp) cc_final: 0.8043 (mm) outliers start: 86 outliers final: 58 residues processed: 289 average time/residue: 0.2607 time to fit residues: 119.8747 Evaluate side-chains 299 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 232 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 284 HIS Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 521 TRP Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 643 ASN Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 284 HIS Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 521 TRP Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 172 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN B 410 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 410 ASN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN A 410 ASN A 452 ASN D 297 ASN D 339 ASN D 410 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18873 Z= 0.282 Angle : 0.527 6.614 25614 Z= 0.273 Chirality : 0.037 0.132 3060 Planarity : 0.003 0.033 3146 Dihedral : 6.759 105.403 2740 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.19 % Favored : 93.77 % Rotamer: Outliers : 5.41 % Allowed : 25.10 % Favored : 69.49 % 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: -0.53 (0.17), residues: 2392 helix: 0.94 (0.14), residues: 1544 sheet: -2.19 (0.49), residues: 52 loop : -2.92 (0.18), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 380 HIS 0.005 0.001 HIS C 301 PHE 0.014 0.001 PHE A 316 TYR 0.017 0.001 TYR D 451 ARG 0.004 0.000 ARG C 693 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 225 time to evaluate : 2.130 Fit side-chains REVERT: B 205 ASN cc_start: 0.8928 (t0) cc_final: 0.8678 (t0) REVERT: B 234 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8418 (mp) REVERT: B 320 MET cc_start: 0.8425 (mmm) cc_final: 0.7758 (mmm) REVERT: B 488 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7753 (mpp) REVERT: B 572 MET cc_start: 0.7502 (mmm) cc_final: 0.6849 (mmp) REVERT: B 643 ASN cc_start: 0.6665 (OUTLIER) cc_final: 0.6063 (p0) REVERT: C 234 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8382 (mp) REVERT: C 320 MET cc_start: 0.8359 (mmm) cc_final: 0.7757 (mmm) REVERT: C 487 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.5321 (mmm160) REVERT: C 488 MET cc_start: 0.8134 (mpp) cc_final: 0.7824 (mpp) REVERT: C 572 MET cc_start: 0.7458 (mmm) cc_final: 0.6856 (mmp) REVERT: C 643 ASN cc_start: 0.6716 (OUTLIER) cc_final: 0.6206 (p0) REVERT: A 234 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8373 (mp) REVERT: A 320 MET cc_start: 0.8431 (mmm) cc_final: 0.7782 (mmm) REVERT: A 358 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8798 (tttp) REVERT: A 488 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7822 (mpp) REVERT: A 572 MET cc_start: 0.7845 (mmm) cc_final: 0.7401 (mmp) REVERT: A 643 ASN cc_start: 0.6831 (OUTLIER) cc_final: 0.6220 (p0) REVERT: D 234 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8288 (mp) REVERT: D 320 MET cc_start: 0.8434 (mmm) cc_final: 0.7781 (mmm) REVERT: D 358 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8764 (tttp) REVERT: D 488 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7764 (mpp) REVERT: D 643 ASN cc_start: 0.6876 (OUTLIER) cc_final: 0.6235 (p0) REVERT: D 652 ILE cc_start: 0.8407 (mp) cc_final: 0.8132 (mm) outliers start: 94 outliers final: 71 residues processed: 293 average time/residue: 0.2537 time to fit residues: 117.8381 Evaluate side-chains 298 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 213 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 284 HIS Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain C residue 521 TRP Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 643 ASN Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 521 TRP Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 232 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18873 Z= 0.179 Angle : 0.462 5.888 25614 Z= 0.243 Chirality : 0.036 0.125 3060 Planarity : 0.003 0.032 3146 Dihedral : 6.381 95.299 2740 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.30 % Allowed : 25.79 % Favored : 68.91 % 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: -0.28 (0.17), residues: 2392 helix: 1.13 (0.14), residues: 1544 sheet: -1.86 (0.51), residues: 52 loop : -2.83 (0.18), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 380 HIS 0.003 0.001 HIS C 301 PHE 0.009 0.001 PHE B 316 TYR 0.020 0.001 TYR A 451 ARG 0.003 0.000 ARG C 693 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 225 time to evaluate : 1.728 Fit side-chains REVERT: B 205 ASN cc_start: 0.8960 (t0) cc_final: 0.8706 (t0) REVERT: B 234 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8409 (mp) REVERT: B 320 MET cc_start: 0.8388 (mmm) cc_final: 0.7667 (mmm) REVERT: B 488 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7730 (mpp) REVERT: B 643 ASN cc_start: 0.6668 (OUTLIER) cc_final: 0.6088 (p0) REVERT: C 234 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8373 (mp) REVERT: C 320 MET cc_start: 0.8311 (mmm) cc_final: 0.7732 (mmm) REVERT: C 488 MET cc_start: 0.8003 (mpp) cc_final: 0.7722 (mpp) REVERT: C 643 ASN cc_start: 0.6655 (OUTLIER) cc_final: 0.6105 (p0) REVERT: A 234 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8398 (mp) REVERT: A 320 MET cc_start: 0.8368 (mmm) cc_final: 0.7684 (mmm) REVERT: A 358 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8781 (tttp) REVERT: A 488 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7797 (mpp) REVERT: A 572 MET cc_start: 0.7831 (mmm) cc_final: 0.7408 (mmp) REVERT: A 643 ASN cc_start: 0.6761 (OUTLIER) cc_final: 0.6108 (p0) REVERT: A 647 ASN cc_start: 0.7925 (t0) cc_final: 0.7513 (t0) REVERT: D 234 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8250 (mp) REVERT: D 320 MET cc_start: 0.8378 (mmm) cc_final: 0.7699 (mmm) REVERT: D 358 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8752 (tttp) REVERT: D 488 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7733 (mpp) REVERT: D 643 ASN cc_start: 0.6827 (OUTLIER) cc_final: 0.6200 (p0) REVERT: D 652 ILE cc_start: 0.8371 (mp) cc_final: 0.8100 (mm) outliers start: 92 outliers final: 66 residues processed: 297 average time/residue: 0.2636 time to fit residues: 124.9065 Evaluate side-chains 304 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 225 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 521 TRP Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 643 ASN Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 521 TRP Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 106 optimal weight: 0.0770 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN D 297 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18873 Z= 0.265 Angle : 0.515 6.104 25614 Z= 0.268 Chirality : 0.037 0.126 3060 Planarity : 0.003 0.033 3146 Dihedral : 6.437 88.474 2740 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 5.12 % Allowed : 26.60 % Favored : 68.28 % 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: -0.33 (0.17), residues: 2392 helix: 1.10 (0.14), residues: 1544 sheet: -1.83 (0.48), residues: 52 loop : -2.85 (0.18), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 380 HIS 0.004 0.001 HIS C 301 PHE 0.021 0.001 PHE D 157 TYR 0.018 0.001 TYR A 451 ARG 0.003 0.000 ARG D 693 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 228 time to evaluate : 2.478 Fit side-chains REVERT: B 205 ASN cc_start: 0.8982 (t0) cc_final: 0.8711 (t0) REVERT: B 234 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8412 (mp) REVERT: B 320 MET cc_start: 0.8428 (mmm) cc_final: 0.7770 (mmm) REVERT: B 488 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7783 (mpp) REVERT: B 572 MET cc_start: 0.7485 (mmm) cc_final: 0.6934 (mmp) REVERT: B 643 ASN cc_start: 0.6738 (OUTLIER) cc_final: 0.6063 (p0) REVERT: C 234 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8377 (mp) REVERT: C 320 MET cc_start: 0.8371 (mmm) cc_final: 0.7767 (mmm) REVERT: C 488 MET cc_start: 0.7988 (mpp) cc_final: 0.7697 (mpp) REVERT: C 643 ASN cc_start: 0.6742 (OUTLIER) cc_final: 0.6100 (p0) REVERT: A 234 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8323 (mp) REVERT: A 320 MET cc_start: 0.8410 (mmm) cc_final: 0.7783 (mmm) REVERT: A 358 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8791 (tttp) REVERT: A 488 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7810 (mpp) REVERT: A 572 MET cc_start: 0.7861 (mmm) cc_final: 0.7432 (mmp) REVERT: A 610 GLU cc_start: 0.8163 (pp20) cc_final: 0.7897 (tm-30) REVERT: A 643 ASN cc_start: 0.6807 (OUTLIER) cc_final: 0.6127 (p0) REVERT: A 647 ASN cc_start: 0.7936 (t0) cc_final: 0.7567 (t0) REVERT: D 234 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8257 (mp) REVERT: D 320 MET cc_start: 0.8412 (mmm) cc_final: 0.7753 (mmm) REVERT: D 358 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8766 (tttp) REVERT: D 488 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7746 (mpp) REVERT: D 643 ASN cc_start: 0.6909 (OUTLIER) cc_final: 0.6222 (p0) REVERT: D 652 ILE cc_start: 0.8385 (mp) cc_final: 0.8121 (mm) outliers start: 89 outliers final: 71 residues processed: 292 average time/residue: 0.2634 time to fit residues: 122.6993 Evaluate side-chains 303 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 219 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 284 HIS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 521 TRP Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 643 ASN Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 521 TRP Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.0754 > 50: distance: 51 - 57: 12.352 distance: 57 - 58: 8.074 distance: 58 - 59: 8.630 distance: 58 - 61: 16.434 distance: 59 - 60: 5.998 distance: 59 - 71: 27.431 distance: 61 - 62: 6.892 distance: 62 - 63: 10.336 distance: 62 - 64: 6.844 distance: 63 - 65: 4.248 distance: 64 - 66: 4.481 distance: 64 - 67: 5.601 distance: 65 - 66: 4.983 distance: 67 - 69: 3.743 distance: 68 - 70: 4.398 distance: 69 - 70: 5.970 distance: 71 - 72: 28.397 distance: 72 - 73: 23.517 distance: 73 - 74: 9.152 distance: 73 - 76: 7.868 distance: 76 - 77: 16.703 distance: 77 - 78: 26.633 distance: 77 - 80: 31.286 distance: 78 - 84: 18.692 distance: 80 - 81: 6.304 distance: 81 - 83: 3.033 distance: 84 - 85: 27.622 distance: 85 - 86: 8.114 distance: 85 - 88: 11.244 distance: 86 - 87: 10.597 distance: 86 - 93: 8.522 distance: 88 - 89: 13.778 distance: 89 - 90: 39.020 distance: 90 - 91: 19.292 distance: 90 - 92: 19.101 distance: 93 - 94: 11.951 distance: 94 - 95: 25.562 distance: 94 - 97: 13.665 distance: 95 - 96: 20.235 distance: 95 - 98: 5.659 distance: 98 - 99: 6.107 distance: 99 - 100: 15.664 distance: 99 - 102: 14.360 distance: 100 - 101: 5.558 distance: 100 - 105: 20.742 distance: 102 - 103: 11.620 distance: 102 - 104: 17.884 distance: 105 - 106: 11.276 distance: 106 - 107: 15.653 distance: 106 - 109: 15.278 distance: 107 - 108: 14.881 distance: 107 - 116: 20.894 distance: 109 - 110: 15.910 distance: 110 - 111: 21.068 distance: 111 - 112: 7.966 distance: 112 - 113: 11.893 distance: 113 - 114: 10.912 distance: 113 - 115: 10.264 distance: 116 - 117: 15.988 distance: 117 - 118: 18.090 distance: 117 - 120: 25.292 distance: 118 - 119: 32.217 distance: 118 - 124: 20.850 distance: 120 - 121: 21.299 distance: 121 - 122: 11.241 distance: 121 - 123: 18.818 distance: 124 - 125: 5.569 distance: 125 - 126: 5.718 distance: 125 - 128: 21.002 distance: 126 - 127: 21.198 distance: 126 - 132: 5.707 distance: 128 - 129: 12.198 distance: 129 - 130: 26.259 distance: 129 - 131: 19.279 distance: 132 - 133: 18.417 distance: 133 - 134: 14.241 distance: 133 - 136: 17.434 distance: 134 - 135: 8.600 distance: 134 - 140: 3.901 distance: 136 - 137: 5.222 distance: 137 - 138: 12.840 distance: 137 - 139: 9.511