Starting phenix.real_space_refine on Wed Mar 20 02:44:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d5c_27208/03_2024/8d5c_27208.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d5c_27208/03_2024/8d5c_27208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d5c_27208/03_2024/8d5c_27208.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d5c_27208/03_2024/8d5c_27208.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d5c_27208/03_2024/8d5c_27208.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d5c_27208/03_2024/8d5c_27208.pdb" } resolution = 3.9 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= 0.002 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 135 5.16 5 C 13464 2.51 5 N 3669 2.21 5 O 4102 1.98 5 H 4739 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "X ASP 612": "OD1" <-> "OD2" Residue "Y PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 584": "OE1" <-> "OE2" Residue "Y TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 634": "OE1" <-> "OE2" Residue "Z TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 55": "OE1" <-> "OE2" Residue "P PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26109 Number of models: 1 Model: "" Number of chains: 15 Chain: "X" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1042 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "Y" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1042 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "Z" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1042 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "A" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2952 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 356} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "B" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2952 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 356} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "C" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2952 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 356} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "H" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1790 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1646 Classifications: {'peptide': 113} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 105} Chain: "I" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1766 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain breaks: 1 Chain: "J" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1646 Classifications: {'peptide': 113} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 105} Chain: "P" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1523 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain breaks: 3 Chain: "Q" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1646 Classifications: {'peptide': 113} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 105} Time building chain proxies: 11.66, per 1000 atoms: 0.45 Number of scatterers: 26109 At special positions: 0 Unit cell: (145.41, 180.93, 198.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 O 4102 8.00 N 3669 7.00 C 13464 6.00 H 4739 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS X 598 " - pdb=" SG CYS X 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 598 " - pdb=" SG CYS Y 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 598 " - pdb=" SG CYS Z 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 605 " - pdb=" SG CYS C 501 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 84 " distance=2.03 Simple disulfide: pdb=" SG CYS D 130 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 16 " - pdb=" SG CYS E 84 " distance=2.03 Simple disulfide: pdb=" SG CYS E 130 " - pdb=" SG CYS E 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 84 " distance=2.03 Simple disulfide: pdb=" SG CYS F 130 " - pdb=" SG CYS F 159 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 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: 14.69 Conformation dependent library (CDL) restraints added in 3.7 seconds 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5050 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 44 sheets defined 19.0% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'X' and resid 529 through 547 removed outlier: 4.109A pdb=" N THR X 538 " --> pdb=" O SER X 534 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL X 539 " --> pdb=" O MET X 535 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY X 547 " --> pdb=" O LEU X 543 " (cutoff:3.500A) Processing helix chain 'X' and resid 568 through 593 removed outlier: 3.782A pdb=" N GLY X 572 " --> pdb=" O LEU X 568 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE X 573 " --> pdb=" O THR X 569 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA X 578 " --> pdb=" O LYS X 574 " (cutoff:3.500A) Processing helix chain 'X' and resid 618 through 625 removed outlier: 3.565A pdb=" N ILE X 622 " --> pdb=" O THR X 618 " (cutoff:3.500A) Processing helix chain 'X' and resid 627 through 635 Processing helix chain 'X' and resid 640 through 664 removed outlier: 3.918A pdb=" N THR X 644 " --> pdb=" O GLN X 640 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU X 663 " --> pdb=" O GLU X 659 " (cutoff:3.500A) Processing helix chain 'Y' and resid 529 through 546 removed outlier: 3.603A pdb=" N THR Y 538 " --> pdb=" O SER Y 534 " (cutoff:3.500A) Processing helix chain 'Y' and resid 565 through 567 No H-bonds generated for 'chain 'Y' and resid 565 through 567' Processing helix chain 'Y' and resid 568 through 593 removed outlier: 3.582A pdb=" N GLY Y 572 " --> pdb=" O LEU Y 568 " (cutoff:3.500A) Processing helix chain 'Y' and resid 618 through 625 removed outlier: 3.731A pdb=" N TRP Y 623 " --> pdb=" O ILE Y 619 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN Y 625 " --> pdb=" O GLU Y 621 " (cutoff:3.500A) Processing helix chain 'Y' and resid 627 through 635 Processing helix chain 'Y' and resid 638 through 664 removed outlier: 3.658A pdb=" N TYR Y 643 " --> pdb=" O THR Y 639 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR Y 644 " --> pdb=" O GLN Y 640 " (cutoff:3.500A) Processing helix chain 'Z' and resid 529 through 546 removed outlier: 3.695A pdb=" N VAL Z 539 " --> pdb=" O MET Z 535 " (cutoff:3.500A) Processing helix chain 'Z' and resid 567 through 593 removed outlier: 4.671A pdb=" N TRP Z 571 " --> pdb=" O GLN Z 567 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA Z 578 " --> pdb=" O LYS Z 574 " (cutoff:3.500A) Processing helix chain 'Z' and resid 618 through 625 Processing helix chain 'Z' and resid 627 through 635 Processing helix chain 'Z' and resid 638 through 664 removed outlier: 3.841A pdb=" N ILE Z 642 " --> pdb=" O TYR Z 638 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR Z 643 " --> pdb=" O THR Z 639 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR Z 644 " --> pdb=" O GLN Z 640 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU Z 662 " --> pdb=" O GLN Z 658 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU Z 663 " --> pdb=" O GLU Z 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 73 Processing helix chain 'A' and resid 100 through 113 removed outlier: 4.101A pdb=" N GLU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 350 removed outlier: 4.185A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.798A pdb=" N THR A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 removed outlier: 4.002A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 65 removed outlier: 3.977A pdb=" N ASP D 63 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY D 65 " --> pdb=" O TRP D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 79 Processing helix chain 'D' and resid 150 through 154 Processing helix chain 'B' and resid 64 through 73 Processing helix chain 'B' and resid 99 through 116 removed outlier: 4.141A pdb=" N GLN B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET B 104 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 351 removed outlier: 4.508A pdb=" N GLU B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 480 Processing helix chain 'E' and resid 75 through 79 removed outlier: 3.656A pdb=" N SER E 79 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 154 Processing helix chain 'C' and resid 64 through 73 Processing helix chain 'C' and resid 100 through 116 removed outlier: 3.667A pdb=" N MET C 104 " --> pdb=" O MET C 100 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 353 removed outlier: 4.616A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR C 341 " --> pdb=" O ARG C 337 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU C 351 " --> pdb=" O ALA C 347 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 4.007A pdb=" N THR C 373 " --> pdb=" O PRO C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 391 removed outlier: 3.526A pdb=" N LEU C 390 " --> pdb=" O THR C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 480 removed outlier: 3.787A pdb=" N ASN C 478 " --> pdb=" O ASN C 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 65 removed outlier: 4.593A pdb=" N ASP F 63 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'F' and resid 150 through 154 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.041A pdb=" N ALA L 83 " --> pdb=" O GLU L 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.738A pdb=" N ASP J 82 " --> pdb=" O GLY J 79 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA J 83 " --> pdb=" O GLU J 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 79 through 83' Processing helix chain 'P' and resid 61 through 64 removed outlier: 4.255A pdb=" N MET P 64 " --> pdb=" O GLU P 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 61 through 64' Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'Q' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'Z' and resid 604 through 609 removed outlier: 3.766A pdb=" N CYS Z 604 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR Z 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL C 36 " --> pdb=" O THR Z 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 39 removed outlier: 4.261A pdb=" N GLY A 495 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.519A pdb=" N LYS A 490 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.539A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.795A pdb=" N VAL A 120 " --> pdb=" O MET A 434 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A 434 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 123 through 126 Processing sheet with id=AA7, first strand: chain 'A' and resid 256 through 257 removed outlier: 3.592A pdb=" N THR A 257 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER A 375 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 384 " --> pdb=" O ARG A 419 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 256 through 257 removed outlier: 3.592A pdb=" N THR A 257 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER A 375 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 384 " --> pdb=" O ARG A 419 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.449A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.466A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.264A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 361 Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 5 removed outlier: 6.310A pdb=" N VAL D 4 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 39 through 40 removed outlier: 3.850A pdb=" N GLN D 40 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 99 through 102 Processing sheet with id=AB4, first strand: chain 'D' and resid 127 through 129 Processing sheet with id=AB5, first strand: chain 'B' and resid 35 through 39 removed outlier: 3.611A pdb=" N GLY B 495 " --> pdb=" O TYR B 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 53 through 55 removed outlier: 3.527A pdb=" N PHE B 53 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS B 218 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.775A pdb=" N ILE B 84 " --> pdb=" O THR B 244 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS B 487 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 196 through 202 removed outlier: 3.994A pdb=" N VAL B 120 " --> pdb=" O MET B 434 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET B 434 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 122 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B 432 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 271 through 273 removed outlier: 9.978A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.529A pdb=" N LEU B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 11.738A pdb=" N LEU B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 10.091A pdb=" N GLU B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLY B 451 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG B 469 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N THR B 357 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE B 468 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 359 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.539A pdb=" N ILE B 333 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE B 414 " --> pdb=" O ILE B 333 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG B 419 " --> pdb=" O TYR B 384 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR B 384 " --> pdb=" O ARG B 419 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 2 through 5 removed outlier: 4.126A pdb=" N LYS E 2 " --> pdb=" O GLU E 92 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS E 29 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TRP E 28 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU E 37 " --> pdb=" O TRP E 28 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 39 through 40 removed outlier: 3.709A pdb=" N GLN E 40 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 99 through 102 removed outlier: 6.523A pdb=" N GLN E 112 " --> pdb=" O GLN E 148 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN E 148 " --> pdb=" O GLN E 112 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 139 through 140 Processing sheet with id=AC6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.574A pdb=" N ILE C 84 " --> pdb=" O THR C 244 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 125 through 126 Processing sheet with id=AC8, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.848A pdb=" N THR C 455 " --> pdb=" O ARG C 469 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG C 469 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.127A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN C 295 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 2 through 6 removed outlier: 3.961A pdb=" N LYS F 2 " --> pdb=" O GLU F 92 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS F 29 " --> pdb=" O ILE F 83 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 12 through 14 Processing sheet with id=AD3, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AD4, first strand: chain 'F' and resid 99 through 102 removed outlier: 6.226A pdb=" N GLN F 112 " --> pdb=" O GLN F 148 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN F 148 " --> pdb=" O GLN F 112 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 139 through 140 Processing sheet with id=AD6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.515A pdb=" N ILE H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU H 46 " --> pdb=" O LYS H 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD9, first strand: chain 'L' and resid 10 through 14 removed outlier: 7.065A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR L 49 " --> pdb=" O ASN L 53 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.578A pdb=" N LEU I 82 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET I 20 " --> pdb=" O MET I 80 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA I 78 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR I 79 " --> pdb=" O THR I 70 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR I 70 " --> pdb=" O TYR I 79 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.102A pdb=" N ILE I 34 " --> pdb=" O ASP I 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE4, first strand: chain 'J' and resid 12 through 14 removed outlier: 6.147A pdb=" N VAL J 13 " --> pdb=" O LYS J 107 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 3 through 6 removed outlier: 3.523A pdb=" N ALA P 78 " --> pdb=" O CYS P 22 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.522A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG P 40 " --> pdb=" O GLY P 44 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'Q' and resid 10 through 14 removed outlier: 3.619A pdb=" N ALA Q 84 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N MET Q 33 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR Q 49 " --> pdb=" O MET Q 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR Q 49 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN Q 53 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) 716 hydrogen bonds defined for protein. 1815 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: 9.05 Time building geometry restraints manager: 15.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4739 1.04 - 1.23: 1539 1.23 - 1.43: 7737 1.43 - 1.63: 12356 1.63 - 1.83: 183 Bond restraints: 26554 Sorted by residual: bond pdb=" C TYR P 52 " pdb=" O TYR P 52 " ideal model delta sigma weight residual 1.249 1.238 0.011 8.50e-03 1.38e+04 1.69e+00 bond pdb=" CA GLY I 44 " pdb=" C GLY I 44 " ideal model delta sigma weight residual 1.514 1.530 -0.015 1.41e-02 5.03e+03 1.19e+00 bond pdb=" CB PRO I 14 " pdb=" CG PRO I 14 " ideal model delta sigma weight residual 1.492 1.545 -0.053 5.00e-02 4.00e+02 1.11e+00 bond pdb=" N GLY I 44 " pdb=" CA GLY I 44 " ideal model delta sigma weight residual 1.449 1.463 -0.014 1.45e-02 4.76e+03 8.94e-01 bond pdb=" C GLN A 428 " pdb=" N GLY A 429 " ideal model delta sigma weight residual 1.331 1.317 0.013 1.46e-02 4.69e+03 8.55e-01 ... (remaining 26549 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.73: 625 106.73 - 113.56: 20564 113.56 - 120.40: 8828 120.40 - 127.24: 9997 127.24 - 134.08: 293 Bond angle restraints: 40307 Sorted by residual: angle pdb=" C ALA A 73 " pdb=" N CYS A 74 " pdb=" CA CYS A 74 " ideal model delta sigma weight residual 122.19 129.88 -7.69 2.30e+00 1.89e-01 1.12e+01 angle pdb=" C ALA C 73 " pdb=" N CYS C 74 " pdb=" CA CYS C 74 " ideal model delta sigma weight residual 121.54 127.77 -6.23 1.91e+00 2.74e-01 1.06e+01 angle pdb=" N GLU D 150 " pdb=" CA GLU D 150 " pdb=" C GLU D 150 " ideal model delta sigma weight residual 108.34 111.59 -3.25 1.31e+00 5.83e-01 6.17e+00 angle pdb=" N PHE H 51 " pdb=" CA PHE H 51 " pdb=" CB PHE H 51 " ideal model delta sigma weight residual 111.20 115.18 -3.98 1.62e+00 3.81e-01 6.03e+00 angle pdb=" N GLY I 106 " pdb=" CA GLY I 106 " pdb=" C GLY I 106 " ideal model delta sigma weight residual 111.85 114.38 -2.53 1.06e+00 8.90e-01 5.70e+00 ... (remaining 40302 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 13663 17.96 - 35.93: 983 35.93 - 53.89: 210 53.89 - 71.86: 63 71.86 - 89.82: 25 Dihedral angle restraints: 14944 sinusoidal: 6650 harmonic: 8294 Sorted by residual: dihedral pdb=" CB CYS B 119 " pdb=" SG CYS B 119 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual -86.00 -170.62 84.62 1 1.00e+01 1.00e-02 8.70e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -169.42 83.42 1 1.00e+01 1.00e-02 8.50e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 170.19 -77.19 1 1.00e+01 1.00e-02 7.47e+01 ... (remaining 14941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2247 0.032 - 0.065: 728 0.065 - 0.097: 167 0.097 - 0.130: 159 0.130 - 0.162: 9 Chirality restraints: 3310 Sorted by residual: chirality pdb=" CA ILE I 48 " pdb=" N ILE I 48 " pdb=" C ILE I 48 " pdb=" CB ILE I 48 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CG LEU I 45 " pdb=" CB LEU I 45 " pdb=" CD1 LEU I 45 " pdb=" CD2 LEU I 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA VAL I 37 " pdb=" N VAL I 37 " pdb=" C VAL I 37 " pdb=" CB VAL I 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 3307 not shown) Planarity restraints: 4424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 51 " -0.024 2.00e-02 2.50e+03 1.67e-02 8.34e+00 pdb=" CG PHE H 51 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE H 51 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE H 51 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE H 51 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 51 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE H 51 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE H 51 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE H 51 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE H 51 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE H 51 " -0.006 2.00e-02 2.50e+03 pdb=" HZ PHE H 51 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 33 " -0.018 2.00e-02 2.50e+03 1.12e-02 5.02e+00 pdb=" CG TRP H 33 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP H 33 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP H 33 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 33 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 33 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 33 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 33 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 33 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 33 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP H 33 " -0.007 2.00e-02 2.50e+03 pdb=" HE1 TRP H 33 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP H 33 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 33 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 33 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP H 33 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 497 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 498 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 498 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 498 " -0.024 5.00e-02 4.00e+02 ... (remaining 4421 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 466 2.17 - 2.78: 22158 2.78 - 3.39: 44282 3.39 - 3.99: 62846 3.99 - 4.60: 89864 Nonbonded interactions: 219616 Sorted by model distance: nonbonded pdb=" OG1 THR I 70 " pdb="HE22 GLN I 81 " model vdw 1.567 1.850 nonbonded pdb=" OD1 ASP Q 27C" pdb=" HG SER Q 31 " model vdw 1.612 1.850 nonbonded pdb=" OE1 GLN I 39 " pdb=" HH TYR I 91 " model vdw 1.639 1.850 nonbonded pdb=" HG1 THR L 20 " pdb=" OD1 ASN L 74 " model vdw 1.643 1.850 nonbonded pdb=" HZ1 LYS J 39 " pdb=" OE1 GLN J 42 " model vdw 1.667 1.850 ... (remaining 219611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'H' and (resid 1 through 71 or resid 76 through 114)) selection = (chain 'I' and (resid 1 through 25 or resid 27 through 93 or (resid 94 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 95 \ through 114)) } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'Q' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 1.260 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: 0.570 Extract box with map and model: 7.280 Check model and map are aligned: 0.390 Set scattering table: 0.260 Process input model: 71.910 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 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 : 0.002 0.053 21815 Z= 0.131 Angle : 0.476 7.689 29603 Z= 0.268 Chirality : 0.040 0.162 3310 Planarity : 0.003 0.043 3790 Dihedral : 13.149 89.821 7924 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 32.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -1.61 (0.16), residues: 2666 helix: 1.65 (0.28), residues: 405 sheet: -0.85 (0.19), residues: 708 loop : -2.02 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP H 33 HIS 0.005 0.001 HIS A 374 PHE 0.049 0.001 PHE H 51 TYR 0.015 0.001 TYR H 97 ARG 0.002 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 311 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7944 (mmm) cc_final: 0.7698 (mmp) REVERT: E 78 ASP cc_start: 0.6339 (t70) cc_final: 0.6095 (t70) REVERT: E 87 GLU cc_start: 0.6528 (tm-30) cc_final: 0.6135 (tm-30) REVERT: F 14 LEU cc_start: 0.5947 (mm) cc_final: 0.5557 (mm) REVERT: F 70 ILE cc_start: 0.6836 (mm) cc_final: 0.6529 (mm) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.3905 time to fit residues: 189.7055 Evaluate side-chains 237 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 134 optimal weight: 0.0020 chunk 106 optimal weight: 3.9990 chunk 206 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 chunk 239 optimal weight: 4.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN A 422 GLN ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 21815 Z= 0.147 Angle : 0.459 7.018 29603 Z= 0.242 Chirality : 0.040 0.139 3310 Planarity : 0.003 0.038 3790 Dihedral : 3.860 32.244 2887 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 33.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.68 % Allowed : 5.95 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -1.64 (0.16), residues: 2666 helix: 1.50 (0.27), residues: 423 sheet: -0.75 (0.20), residues: 702 loop : -2.10 (0.15), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 33 HIS 0.010 0.001 HIS P 43 PHE 0.021 0.001 PHE H 51 TYR 0.017 0.001 TYR H 97 ARG 0.003 0.000 ARG C 419 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 249 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 584 GLU cc_start: 0.8115 (tp30) cc_final: 0.7913 (tp30) REVERT: Y 644 THR cc_start: 0.7759 (p) cc_final: 0.7492 (t) REVERT: Z 589 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6980 (t0) REVERT: A 475 MET cc_start: 0.7609 (mmm) cc_final: 0.7349 (mmp) REVERT: E 78 ASP cc_start: 0.6355 (t70) cc_final: 0.6122 (t70) REVERT: E 87 GLU cc_start: 0.6792 (tm-30) cc_final: 0.6137 (tm-30) REVERT: P 6 GLN cc_start: 0.6160 (mt0) cc_final: 0.5798 (mt0) outliers start: 16 outliers final: 12 residues processed: 261 average time/residue: 0.4001 time to fit residues: 165.1637 Evaluate side-chains 247 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 234 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain X residue 648 VAL Chi-restraints excluded: chain Y residue 539 VAL Chi-restraints excluded: chain Z residue 568 LEU Chi-restraints excluded: chain Z residue 589 ASP Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 199 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 chunk 259 optimal weight: 0.7980 chunk 213 optimal weight: 8.9990 chunk 238 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 192 optimal weight: 30.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 21815 Z= 0.152 Angle : 0.452 5.922 29603 Z= 0.236 Chirality : 0.040 0.156 3310 Planarity : 0.003 0.035 3790 Dihedral : 3.851 30.955 2887 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 34.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.93 % Allowed : 8.44 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -1.57 (0.16), residues: 2666 helix: 1.82 (0.27), residues: 405 sheet: -0.73 (0.19), residues: 768 loop : -2.13 (0.15), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 96 HIS 0.007 0.001 HIS A 66 PHE 0.013 0.001 PHE H 51 TYR 0.017 0.001 TYR H 97 ARG 0.002 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 244 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 537 LEU cc_start: 0.6750 (tp) cc_final: 0.6485 (tt) REVERT: Y 644 THR cc_start: 0.7805 (p) cc_final: 0.7544 (t) REVERT: Z 589 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.7103 (t0) REVERT: A 475 MET cc_start: 0.7625 (mmm) cc_final: 0.7363 (mmp) REVERT: E 87 GLU cc_start: 0.6858 (tm-30) cc_final: 0.6211 (tm-30) REVERT: C 475 MET cc_start: 0.7333 (tpp) cc_final: 0.6880 (tpp) REVERT: Q 27 GLN cc_start: 0.1318 (tm-30) cc_final: 0.1082 (tm-30) outliers start: 22 outliers final: 18 residues processed: 257 average time/residue: 0.4055 time to fit residues: 165.4745 Evaluate side-chains 253 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 234 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain X residue 648 VAL Chi-restraints excluded: chain Z residue 568 LEU Chi-restraints excluded: chain Z residue 589 ASP Chi-restraints excluded: chain Z residue 619 ILE Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 161 optimal weight: 0.4980 chunk 241 optimal weight: 6.9990 chunk 255 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 567 GLN ** Z 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN D 27 HIS ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21815 Z= 0.306 Angle : 0.580 8.774 29603 Z= 0.304 Chirality : 0.043 0.168 3310 Planarity : 0.004 0.035 3790 Dihedral : 4.512 33.017 2887 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 40.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.42 % Favored : 87.58 % Rotamer: Outliers : 1.81 % Allowed : 10.42 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -1.88 (0.16), residues: 2666 helix: 1.29 (0.27), residues: 408 sheet: -0.84 (0.20), residues: 696 loop : -2.25 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 112 HIS 0.009 0.001 HIS B 66 PHE 0.019 0.002 PHE A 53 TYR 0.021 0.002 TYR H 97 ARG 0.005 0.001 ARG C 503 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 243 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 644 THR cc_start: 0.7805 (p) cc_final: 0.7600 (t) REVERT: Z 589 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7301 (t0) REVERT: A 479 TRP cc_start: 0.7354 (m-10) cc_final: 0.6681 (m-10) REVERT: E 87 GLU cc_start: 0.7028 (tm-30) cc_final: 0.6302 (tm-30) REVERT: C 294 ILE cc_start: 0.6188 (tt) cc_final: 0.5735 (tt) REVERT: C 475 MET cc_start: 0.7864 (tpp) cc_final: 0.7317 (tpp) REVERT: P 6 GLN cc_start: 0.6309 (mt0) cc_final: 0.5975 (mt0) outliers start: 43 outliers final: 30 residues processed: 269 average time/residue: 0.3966 time to fit residues: 168.4527 Evaluate side-chains 260 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 229 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 584 GLU Chi-restraints excluded: chain X residue 648 VAL Chi-restraints excluded: chain Y residue 573 ILE Chi-restraints excluded: chain Z residue 568 LEU Chi-restraints excluded: chain Z residue 589 ASP Chi-restraints excluded: chain Z residue 619 ILE Chi-restraints excluded: chain Z residue 637 ASN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 63 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 6.9990 chunk 144 optimal weight: 0.0470 chunk 3 optimal weight: 0.0970 chunk 190 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 217 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 overall best weight: 1.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21815 Z= 0.184 Angle : 0.486 7.515 29603 Z= 0.254 Chirality : 0.041 0.146 3310 Planarity : 0.003 0.032 3790 Dihedral : 4.241 32.296 2887 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 37.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 1.60 % Allowed : 12.70 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -1.76 (0.16), residues: 2666 helix: 1.59 (0.27), residues: 405 sheet: -0.85 (0.20), residues: 702 loop : -2.19 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 33 HIS 0.007 0.001 HIS A 66 PHE 0.012 0.001 PHE A 53 TYR 0.020 0.001 TYR H 97 ARG 0.003 0.000 ARG C 503 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 240 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 644 THR cc_start: 0.7706 (p) cc_final: 0.7478 (t) REVERT: Z 589 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7204 (t0) REVERT: A 475 MET cc_start: 0.7682 (mmm) cc_final: 0.7248 (mmp) REVERT: A 479 TRP cc_start: 0.7254 (m-10) cc_final: 0.6570 (m-10) REVERT: E 87 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6282 (tm-30) REVERT: C 475 MET cc_start: 0.7846 (tpp) cc_final: 0.7238 (tpp) REVERT: Q 27 GLN cc_start: 0.1453 (tm-30) cc_final: 0.1072 (tp40) outliers start: 38 outliers final: 29 residues processed: 266 average time/residue: 0.4062 time to fit residues: 174.6378 Evaluate side-chains 261 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 231 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 570 VAL Chi-restraints excluded: chain X residue 584 GLU Chi-restraints excluded: chain X residue 648 VAL Chi-restraints excluded: chain Y residue 548 ILE Chi-restraints excluded: chain Z residue 568 LEU Chi-restraints excluded: chain Z residue 589 ASP Chi-restraints excluded: chain Z residue 595 ILE Chi-restraints excluded: chain Z residue 637 ASN Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 30.0000 chunk 229 optimal weight: 10.0000 chunk 50 optimal weight: 0.0670 chunk 149 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 255 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 50.0000 chunk 134 optimal weight: 2.9990 overall best weight: 1.7124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 616 ASN ** Z 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 43 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21815 Z= 0.198 Angle : 0.487 7.031 29603 Z= 0.256 Chirality : 0.041 0.154 3310 Planarity : 0.003 0.033 3790 Dihedral : 4.206 31.518 2887 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 37.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 1.77 % Allowed : 13.46 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -1.76 (0.16), residues: 2666 helix: 1.57 (0.27), residues: 408 sheet: -0.83 (0.20), residues: 702 loop : -2.20 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 96 HIS 0.006 0.001 HIS A 66 PHE 0.027 0.001 PHE P 63 TYR 0.019 0.001 TYR H 97 ARG 0.003 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 241 time to evaluate : 2.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 644 THR cc_start: 0.7718 (p) cc_final: 0.7483 (t) REVERT: Z 589 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7252 (t0) REVERT: Z 633 LYS cc_start: 0.6990 (pttt) cc_final: 0.6447 (ptmt) REVERT: A 475 MET cc_start: 0.7710 (mmm) cc_final: 0.7253 (mmp) REVERT: A 479 TRP cc_start: 0.7246 (m-10) cc_final: 0.6499 (m-10) REVERT: E 87 GLU cc_start: 0.6954 (tm-30) cc_final: 0.6367 (tm-30) REVERT: C 96 TRP cc_start: 0.6552 (p90) cc_final: 0.6274 (p90) REVERT: Q 27 GLN cc_start: 0.1566 (tm-30) cc_final: 0.1156 (tp40) outliers start: 42 outliers final: 35 residues processed: 270 average time/residue: 0.4149 time to fit residues: 176.8944 Evaluate side-chains 268 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 232 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 570 VAL Chi-restraints excluded: chain X residue 584 GLU Chi-restraints excluded: chain X residue 648 VAL Chi-restraints excluded: chain Y residue 573 ILE Chi-restraints excluded: chain Z residue 568 LEU Chi-restraints excluded: chain Z residue 589 ASP Chi-restraints excluded: chain Z residue 595 ILE Chi-restraints excluded: chain Z residue 619 ILE Chi-restraints excluded: chain Z residue 637 ASN Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 30 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 9.9990 chunk 28 optimal weight: 0.4980 chunk 145 optimal weight: 0.0870 chunk 186 optimal weight: 30.0000 chunk 144 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 254 optimal weight: 20.0000 chunk 159 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21815 Z= 0.211 Angle : 0.498 7.016 29603 Z= 0.261 Chirality : 0.041 0.150 3310 Planarity : 0.003 0.031 3790 Dihedral : 4.268 31.265 2887 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 38.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 2.15 % Allowed : 14.43 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -1.79 (0.16), residues: 2666 helix: 1.59 (0.27), residues: 408 sheet: -0.88 (0.20), residues: 714 loop : -2.22 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 28 HIS 0.005 0.001 HIS A 66 PHE 0.020 0.001 PHE P 63 TYR 0.020 0.001 TYR H 97 ARG 0.004 0.000 ARG C 503 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 294 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 243 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 644 THR cc_start: 0.7719 (p) cc_final: 0.7494 (t) REVERT: Z 589 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7259 (t0) REVERT: Z 633 LYS cc_start: 0.7081 (pttt) cc_final: 0.6576 (ptmt) REVERT: A 475 MET cc_start: 0.7726 (mmm) cc_final: 0.7236 (mmp) REVERT: A 479 TRP cc_start: 0.7251 (m-10) cc_final: 0.6369 (m-10) REVERT: E 87 GLU cc_start: 0.6937 (tm-30) cc_final: 0.6330 (tm-30) REVERT: Q 27 GLN cc_start: 0.1615 (tm-30) cc_final: 0.1120 (tp40) outliers start: 51 outliers final: 42 residues processed: 280 average time/residue: 0.3906 time to fit residues: 172.7549 Evaluate side-chains 278 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 235 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 570 VAL Chi-restraints excluded: chain X residue 584 GLU Chi-restraints excluded: chain X residue 648 VAL Chi-restraints excluded: chain Y residue 573 ILE Chi-restraints excluded: chain Z residue 568 LEU Chi-restraints excluded: chain Z residue 589 ASP Chi-restraints excluded: chain Z residue 595 ILE Chi-restraints excluded: chain Z residue 619 ILE Chi-restraints excluded: chain Z residue 637 ASN Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain Q residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.0470 chunk 101 optimal weight: 0.0570 chunk 151 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 173 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 21815 Z= 0.128 Angle : 0.445 6.132 29603 Z= 0.232 Chirality : 0.040 0.143 3310 Planarity : 0.003 0.030 3790 Dihedral : 3.927 29.688 2887 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 36.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 1.05 % Allowed : 15.70 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -1.59 (0.17), residues: 2666 helix: 1.93 (0.27), residues: 405 sheet: -0.72 (0.19), residues: 780 loop : -2.20 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 28 HIS 0.005 0.001 HIS A 66 PHE 0.026 0.001 PHE I 100E TYR 0.016 0.001 TYR H 97 ARG 0.002 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 238 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 566 LEU cc_start: 0.7131 (mm) cc_final: 0.6856 (mt) REVERT: Y 644 THR cc_start: 0.7704 (p) cc_final: 0.7405 (t) REVERT: Z 589 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7231 (t0) REVERT: Z 633 LYS cc_start: 0.7046 (pttt) cc_final: 0.6531 (ptmt) REVERT: A 475 MET cc_start: 0.7625 (mmm) cc_final: 0.7167 (mmt) REVERT: A 479 TRP cc_start: 0.7157 (m-10) cc_final: 0.6417 (m-10) REVERT: E 87 GLU cc_start: 0.6800 (tm-30) cc_final: 0.6306 (tm-30) REVERT: C 475 MET cc_start: 0.7445 (mmm) cc_final: 0.6975 (tpp) REVERT: Q 27 GLN cc_start: 0.1621 (tm-30) cc_final: 0.1273 (tp40) outliers start: 25 outliers final: 21 residues processed: 255 average time/residue: 0.4105 time to fit residues: 164.7084 Evaluate side-chains 259 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 237 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 584 GLU Chi-restraints excluded: chain X residue 648 VAL Chi-restraints excluded: chain Y residue 573 ILE Chi-restraints excluded: chain Z residue 568 LEU Chi-restraints excluded: chain Z residue 589 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain H residue 63 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 10.0000 chunk 222 optimal weight: 0.9990 chunk 237 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 186 optimal weight: 30.0000 chunk 72 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 chunk 224 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21815 Z= 0.247 Angle : 0.519 6.881 29603 Z= 0.272 Chirality : 0.042 0.154 3310 Planarity : 0.003 0.078 3790 Dihedral : 4.304 30.969 2887 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 40.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.08 % Favored : 87.92 % Rotamer: Outliers : 1.48 % Allowed : 15.65 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -1.78 (0.16), residues: 2666 helix: 1.62 (0.27), residues: 408 sheet: -0.82 (0.20), residues: 708 loop : -2.26 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 96 HIS 0.005 0.001 HIS J 76 PHE 0.019 0.002 PHE I 100E TYR 0.020 0.001 TYR H 97 ARG 0.006 0.000 ARG J 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 241 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 644 THR cc_start: 0.7737 (p) cc_final: 0.7513 (t) REVERT: Z 589 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7370 (t0) REVERT: Z 633 LYS cc_start: 0.7121 (pttt) cc_final: 0.6618 (ptmt) REVERT: A 479 TRP cc_start: 0.7316 (m-10) cc_final: 0.6466 (m-10) REVERT: D 166 LYS cc_start: 0.6980 (mmtt) cc_final: 0.6633 (tttm) REVERT: E 87 GLU cc_start: 0.6977 (tm-30) cc_final: 0.6367 (tm-30) REVERT: C 294 ILE cc_start: 0.6157 (tt) cc_final: 0.5754 (tt) REVERT: C 475 MET cc_start: 0.7678 (mmm) cc_final: 0.7159 (tpp) REVERT: J 49 TYR cc_start: 0.6235 (p90) cc_final: 0.4387 (p90) REVERT: P 40 ARG cc_start: 0.6000 (tmm-80) cc_final: 0.5787 (tmm-80) REVERT: Q 27 GLN cc_start: 0.1715 (tm-30) cc_final: 0.1193 (tp40) outliers start: 35 outliers final: 30 residues processed: 266 average time/residue: 0.4014 time to fit residues: 167.0645 Evaluate side-chains 269 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 238 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 584 GLU Chi-restraints excluded: chain X residue 648 VAL Chi-restraints excluded: chain Y residue 573 ILE Chi-restraints excluded: chain Z residue 568 LEU Chi-restraints excluded: chain Z residue 589 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain Q residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 263 optimal weight: 20.0000 chunk 242 optimal weight: 6.9990 chunk 209 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 161 optimal weight: 9.9990 chunk 128 optimal weight: 0.1980 chunk 166 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 21815 Z= 0.135 Angle : 0.456 7.240 29603 Z= 0.238 Chirality : 0.040 0.146 3310 Planarity : 0.003 0.029 3790 Dihedral : 3.990 30.432 2887 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 36.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 1.01 % Allowed : 15.74 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -1.60 (0.17), residues: 2666 helix: 1.88 (0.27), residues: 405 sheet: -0.71 (0.19), residues: 780 loop : -2.22 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 96 HIS 0.004 0.001 HIS A 66 PHE 0.016 0.001 PHE I 100E TYR 0.017 0.001 TYR H 97 ARG 0.002 0.000 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 239 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 566 LEU cc_start: 0.7333 (mm) cc_final: 0.7118 (mt) REVERT: Y 644 THR cc_start: 0.7706 (p) cc_final: 0.7416 (t) REVERT: Z 589 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7330 (t0) REVERT: Z 633 LYS cc_start: 0.7101 (pttt) cc_final: 0.6587 (ptmt) REVERT: A 479 TRP cc_start: 0.7161 (m-10) cc_final: 0.6417 (m-10) REVERT: D 166 LYS cc_start: 0.6872 (mmtt) cc_final: 0.6416 (tttm) REVERT: E 87 GLU cc_start: 0.6783 (tm-30) cc_final: 0.6295 (tm-30) REVERT: C 475 MET cc_start: 0.7460 (mmm) cc_final: 0.6971 (tpp) REVERT: J 49 TYR cc_start: 0.6152 (p90) cc_final: 0.4210 (p90) REVERT: Q 27 GLN cc_start: 0.1695 (tm-30) cc_final: 0.1308 (tp40) REVERT: Q 103 MET cc_start: 0.3484 (tmm) cc_final: 0.3188 (tmm) outliers start: 24 outliers final: 23 residues processed: 256 average time/residue: 0.4111 time to fit residues: 163.9451 Evaluate side-chains 262 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 238 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 584 GLU Chi-restraints excluded: chain X residue 648 VAL Chi-restraints excluded: chain Y residue 573 ILE Chi-restraints excluded: chain Z residue 568 LEU Chi-restraints excluded: chain Z residue 589 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain Q residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 193 optimal weight: 8.9990 chunk 30 optimal weight: 0.0170 chunk 58 optimal weight: 0.9990 chunk 209 optimal weight: 0.2980 chunk 87 optimal weight: 30.0000 chunk 215 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 184 optimal weight: 20.0000 overall best weight: 0.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.167410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.145320 restraints weight = 85136.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.148469 restraints weight = 139733.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.148604 restraints weight = 53640.563| |-----------------------------------------------------------------------------| r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21815 Z= 0.134 Angle : 0.443 7.362 29603 Z= 0.231 Chirality : 0.040 0.141 3310 Planarity : 0.003 0.040 3790 Dihedral : 3.807 29.193 2887 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 36.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 1.22 % Allowed : 15.49 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -1.52 (0.17), residues: 2666 helix: 2.05 (0.27), residues: 405 sheet: -0.64 (0.19), residues: 780 loop : -2.20 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 96 HIS 0.005 0.001 HIS A 374 PHE 0.013 0.001 PHE I 100E TYR 0.016 0.001 TYR H 97 ARG 0.002 0.000 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4987.54 seconds wall clock time: 90 minutes 53.98 seconds (5453.98 seconds total)