Starting phenix.real_space_refine on Wed Feb 21 21:21:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uv5_20904/02_2024/6uv5_20904_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uv5_20904/02_2024/6uv5_20904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uv5_20904/02_2024/6uv5_20904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uv5_20904/02_2024/6uv5_20904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uv5_20904/02_2024/6uv5_20904_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uv5_20904/02_2024/6uv5_20904_updated.pdb" } resolution = 3.4 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 P 15 5.49 5 S 181 5.16 5 C 20403 2.51 5 N 5395 2.21 5 O 5960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 13": "OE1" <-> "OE2" Residue "A PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 781": "OE1" <-> "OE2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A GLU 866": "OE1" <-> "OE2" Residue "A ARG 986": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A GLU 1009": "OE1" <-> "OE2" Residue "A ARG 1045": "NH1" <-> "NH2" Residue "A GLU 1046": "OE1" <-> "OE2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B GLU 547": "OE1" <-> "OE2" Residue "B ARG 576": "NH1" <-> "NH2" Residue "B GLU 584": "OE1" <-> "OE2" Residue "B GLU 781": "OE1" <-> "OE2" Residue "B GLU 795": "OE1" <-> "OE2" Residue "B ARG 848": "NH1" <-> "NH2" Residue "B ARG 986": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B PHE 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1045": "NH1" <-> "NH2" Residue "B ARG 1085": "NH1" <-> "NH2" Residue "B GLU 1097": "OE1" <-> "OE2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C GLU 13": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "C GLU 245": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C GLU 300": "OE1" <-> "OE2" Residue "C GLU 313": "OE1" <-> "OE2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C GLU 523": "OE1" <-> "OE2" Residue "C GLU 547": "OE1" <-> "OE2" Residue "C ARG 576": "NH1" <-> "NH2" Residue "C GLU 584": "OE1" <-> "OE2" Residue "C GLU 599": "OE1" <-> "OE2" Residue "C GLU 603": "OE1" <-> "OE2" Residue "C GLU 770": "OE1" <-> "OE2" Residue "C GLU 781": "OE1" <-> "OE2" Residue "C GLU 795": "OE1" <-> "OE2" Residue "C GLU 802": "OE1" <-> "OE2" Residue "C ARG 848": "NH1" <-> "NH2" Residue "C TYR 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 986": "NH1" <-> "NH2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C TYR 1006": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1043": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1045": "NH1" <-> "NH2" Residue "C ARG 1085": "NH1" <-> "NH2" Residue "D GLU 8": "OE1" <-> "OE2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D GLU 137": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D GLU 300": "OE1" <-> "OE2" Residue "D GLU 370": "OE1" <-> "OE2" Residue "D GLU 386": "OE1" <-> "OE2" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D GLU 408": "OE1" <-> "OE2" Residue "D GLU 547": "OE1" <-> "OE2" Residue "D GLU 584": "OE1" <-> "OE2" Residue "D GLU 733": "OE1" <-> "OE2" Residue "D GLU 781": "OE1" <-> "OE2" Residue "D GLU 792": "OE1" <-> "OE2" Residue "D GLU 851": "OE1" <-> "OE2" Residue "D GLU 866": "OE1" <-> "OE2" Residue "D ARG 986": "NH1" <-> "NH2" Residue "D ARG 995": "NH1" <-> "NH2" Residue "D TYR 1006": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1045": "NH1" <-> "NH2" Residue "D GLU 1046": "OE1" <-> "OE2" Residue "D ARG 1085": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31954 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "B" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "C" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "D" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "A" Number of atoms: 171 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 120 Unusual residues: {'ACO': 2, 'OAA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 120 Unusual residues: {'ACO': 2, 'OAA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 69 Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'ACO': 1, 'OAA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'OAA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'ACO': 1, 'OAA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C AACO A1202 " occ=0.50 ... (100 atoms not shown) pdb=" S1PBACO A1202 " occ=0.50 Time building chain proxies: 30.07, per 1000 atoms: 0.94 Number of scatterers: 31954 At special positions: 0 Unit cell: (140.07, 170.52, 173.13, 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 181 16.00 P 15 15.00 O 5960 8.00 N 5395 7.00 C 20403 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.42 Conformation dependent library (CDL) restraints added in 11.5 seconds 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7392 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 160 helices and 32 sheets defined 38.5% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.64 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 41 through 46 Processing helix chain 'A' and resid 48 through 51 removed outlier: 4.069A pdb=" N LEU A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 78 through 85 Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 182 through 193 Processing helix chain 'A' and resid 226 through 229 No H-bonds generated for 'chain 'A' and resid 226 through 229' Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 282 through 294 Processing helix chain 'A' and resid 313 through 327 removed outlier: 3.651A pdb=" N LEU A 326 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N MET A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 363 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 398 Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.688A pdb=" N VAL A 415 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 518 Processing helix chain 'A' and resid 556 through 562 Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.764A pdb=" N ASN A 587 " --> pdb=" O MET A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 Processing helix chain 'A' and resid 643 through 648 Processing helix chain 'A' and resid 665 through 677 removed outlier: 3.980A pdb=" N GLU A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 706 removed outlier: 4.086A pdb=" N ARG A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 732 Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 772 through 780 Processing helix chain 'A' and resid 793 through 806 Processing helix chain 'A' and resid 825 through 828 No H-bonds generated for 'chain 'A' and resid 825 through 828' Processing helix chain 'A' and resid 859 through 864 Processing helix chain 'A' and resid 869 through 876 Processing helix chain 'A' and resid 884 through 896 removed outlier: 3.861A pdb=" N GLN A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 915 Processing helix chain 'A' and resid 920 through 930 removed outlier: 4.746A pdb=" N THR A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 952 removed outlier: 3.699A pdb=" N PHE A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 952 " --> pdb=" O LYS A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 964 removed outlier: 3.879A pdb=" N ASN A 961 " --> pdb=" O MET A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1002 through 1017 removed outlier: 3.554A pdb=" N SER A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1039 removed outlier: 4.034A pdb=" N GLY A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1054 Processing helix chain 'A' and resid 1056 through 1078 removed outlier: 4.298A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1090 No H-bonds generated for 'chain 'A' and resid 1088 through 1090' Processing helix chain 'B' and resid 8 through 18 Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 78 through 86 removed outlier: 4.525A pdb=" N LEU B 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 223 through 233 removed outlier: 3.885A pdb=" N ASP B 226 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR B 227 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS B 230 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL B 231 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TRP B 233 " --> pdb=" O LYS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 258 Processing helix chain 'B' and resid 282 through 294 Processing helix chain 'B' and resid 313 through 326 Processing helix chain 'B' and resid 350 through 371 removed outlier: 3.655A pdb=" N TYR B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLY B 366 " --> pdb=" O ARG B 362 " (cutoff:3.500A) Proline residue: B 367 - end of helix Processing helix chain 'B' and resid 385 through 398 Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 506 through 518 Processing helix chain 'B' and resid 557 through 562 Processing helix chain 'B' and resid 578 through 587 removed outlier: 3.924A pdb=" N ASN B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 616 Processing helix chain 'B' and resid 643 through 648 Processing helix chain 'B' and resid 664 through 677 removed outlier: 4.205A pdb=" N ASN B 668 " --> pdb=" O GLY B 664 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU B 669 " --> pdb=" O GLY B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 706 removed outlier: 3.968A pdb=" N ARG B 703 " --> pdb=" O ASP B 699 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 706 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 732 Processing helix chain 'B' and resid 772 through 780 Processing helix chain 'B' and resid 793 through 806 Processing helix chain 'B' and resid 825 through 830 Processing helix chain 'B' and resid 859 through 864 Processing helix chain 'B' and resid 869 through 876 Processing helix chain 'B' and resid 884 through 895 removed outlier: 3.792A pdb=" N GLN B 888 " --> pdb=" O LYS B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 915 Processing helix chain 'B' and resid 920 through 930 removed outlier: 4.769A pdb=" N THR B 930 " --> pdb=" O SER B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 952 removed outlier: 3.824A pdb=" N PHE B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 966 removed outlier: 3.684A pdb=" N GLU B 966 " --> pdb=" O LYS B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 996 Processing helix chain 'B' and resid 1002 through 1017 Processing helix chain 'B' and resid 1025 through 1039 Processing helix chain 'B' and resid 1050 through 1054 Processing helix chain 'B' and resid 1058 through 1078 removed outlier: 4.222A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1090 No H-bonds generated for 'chain 'B' and resid 1088 through 1090' Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 48 through 51 removed outlier: 4.489A pdb=" N LEU C 51 " --> pdb=" O PRO C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 180 through 192 Processing helix chain 'C' and resid 223 through 229 removed outlier: 3.676A pdb=" N ASP C 226 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TYR C 227 " --> pdb=" O THR C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 257 Processing helix chain 'C' and resid 282 through 294 Processing helix chain 'C' and resid 313 through 325 Processing helix chain 'C' and resid 350 through 370 removed outlier: 3.733A pdb=" N TYR C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY C 366 " --> pdb=" O ARG C 362 " (cutoff:3.500A) Proline residue: C 367 - end of helix Processing helix chain 'C' and resid 385 through 398 Processing helix chain 'C' and resid 412 through 418 Processing helix chain 'C' and resid 506 through 518 Processing helix chain 'C' and resid 557 through 562 removed outlier: 3.610A pdb=" N LYS C 562 " --> pdb=" O ASP C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 587 removed outlier: 3.914A pdb=" N ASN C 587 " --> pdb=" O MET C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 616 Processing helix chain 'C' and resid 643 through 649 Processing helix chain 'C' and resid 667 through 677 Processing helix chain 'C' and resid 697 through 704 removed outlier: 3.679A pdb=" N ARG C 703 " --> pdb=" O ASP C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 732 Processing helix chain 'C' and resid 768 through 770 No H-bonds generated for 'chain 'C' and resid 768 through 770' Processing helix chain 'C' and resid 772 through 780 Processing helix chain 'C' and resid 793 through 804 Processing helix chain 'C' and resid 825 through 830 Processing helix chain 'C' and resid 859 through 864 Processing helix chain 'C' and resid 869 through 876 Processing helix chain 'C' and resid 884 through 896 removed outlier: 3.805A pdb=" N GLN C 888 " --> pdb=" O LYS C 884 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 889 " --> pdb=" O TYR C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 915 Processing helix chain 'C' and resid 920 through 930 removed outlier: 4.691A pdb=" N THR C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 950 removed outlier: 3.679A pdb=" N PHE C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 966 removed outlier: 4.076A pdb=" N ASN C 961 " --> pdb=" O MET C 957 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU C 966 " --> pdb=" O LYS C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 996 Processing helix chain 'C' and resid 1002 through 1017 removed outlier: 3.593A pdb=" N SER C1016 " --> pdb=" O LYS C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1025 through 1039 removed outlier: 3.543A pdb=" N GLY C1030 " --> pdb=" O ASP C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1054 Processing helix chain 'C' and resid 1058 through 1078 removed outlier: 4.253A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY C1068 " --> pdb=" O GLY C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1088 through 1090 No H-bonds generated for 'chain 'C' and resid 1088 through 1090' Processing helix chain 'D' and resid 8 through 18 Processing helix chain 'D' and resid 41 through 46 Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 66 through 69 No H-bonds generated for 'chain 'D' and resid 66 through 69' Processing helix chain 'D' and resid 78 through 84 Processing helix chain 'D' and resid 115 through 117 No H-bonds generated for 'chain 'D' and resid 115 through 117' Processing helix chain 'D' and resid 162 through 167 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 182 through 193 Processing helix chain 'D' and resid 223 through 233 removed outlier: 3.622A pdb=" N ASP D 226 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR D 227 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LYS D 230 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL D 231 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TRP D 233 " --> pdb=" O LYS D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 255 Processing helix chain 'D' and resid 283 through 294 Processing helix chain 'D' and resid 313 through 325 Processing helix chain 'D' and resid 350 through 363 Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 385 through 398 Processing helix chain 'D' and resid 413 through 418 Processing helix chain 'D' and resid 506 through 518 Processing helix chain 'D' and resid 556 through 562 Processing helix chain 'D' and resid 578 through 587 removed outlier: 3.682A pdb=" N ASN D 587 " --> pdb=" O MET D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 616 Processing helix chain 'D' and resid 643 through 648 Processing helix chain 'D' and resid 665 through 677 removed outlier: 3.585A pdb=" N GLU D 669 " --> pdb=" O GLY D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 705 removed outlier: 3.758A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 732 Processing helix chain 'D' and resid 772 through 780 Processing helix chain 'D' and resid 790 through 804 removed outlier: 4.620A pdb=" N GLY D 794 " --> pdb=" O ASP D 791 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU D 795 " --> pdb=" O GLU D 792 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 797 " --> pdb=" O GLY D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 830 Processing helix chain 'D' and resid 859 through 864 Processing helix chain 'D' and resid 869 through 876 Processing helix chain 'D' and resid 884 through 896 removed outlier: 3.856A pdb=" N GLN D 888 " --> pdb=" O LYS D 884 " (cutoff:3.500A) Processing helix chain 'D' and resid 905 through 915 Processing helix chain 'D' and resid 920 through 930 removed outlier: 4.607A pdb=" N THR D 930 " --> pdb=" O SER D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 952 removed outlier: 3.886A pdb=" N PHE D 946 " --> pdb=" O ALA D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 966 removed outlier: 3.855A pdb=" N ASN D 961 " --> pdb=" O MET D 957 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU D 966 " --> pdb=" O LYS D 962 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 996 Processing helix chain 'D' and resid 1002 through 1017 removed outlier: 3.524A pdb=" N SER D1016 " --> pdb=" O LYS D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1025 through 1037 removed outlier: 3.947A pdb=" N GLY D1030 " --> pdb=" O ASP D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1051 through 1054 No H-bonds generated for 'chain 'D' and resid 1051 through 1054' Processing helix chain 'D' and resid 1058 through 1078 removed outlier: 4.280A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1088 through 1090 No H-bonds generated for 'chain 'D' and resid 1088 through 1090' Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 removed outlier: 5.242A pdb=" N ASP A 222 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE A 197 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR A 198 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 32 through 34 Processing sheet with id= C, first strand: chain 'A' and resid 92 through 95 Processing sheet with id= D, first strand: chain 'A' and resid 205 through 207 Processing sheet with id= E, first strand: chain 'A' and resid 263 through 268 Processing sheet with id= F, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.351A pdb=" N ILE A 337 " --> pdb=" O TRP A 276 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 619 through 621 removed outlier: 7.718A pdb=" N VAL A 501 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N MET A 529 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 14.270A pdb=" N ALA A 527 " --> pdb=" O GLU A 547 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N LEU A 549 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N MET A 529 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 739 through 744 removed outlier: 7.769A pdb=" N TYR A 659 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY A 684 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N SER A 661 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA A 686 " --> pdb=" O SER A 661 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 3 through 5 removed outlier: 5.356A pdb=" N ASP B 222 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE B 197 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N THR B 198 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 129 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 31 through 34 Processing sheet with id= K, first strand: chain 'B' and resid 93 through 95 Processing sheet with id= L, first strand: chain 'B' and resid 205 through 207 Processing sheet with id= M, first strand: chain 'B' and resid 263 through 268 Processing sheet with id= N, first strand: chain 'B' and resid 275 through 277 removed outlier: 6.100A pdb=" N ILE B 337 " --> pdb=" O TRP B 276 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 537 through 543 removed outlier: 8.590A pdb=" N ALA B 527 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ALA B 499 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET B 529 " --> pdb=" O ALA B 499 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL B 501 " --> pdb=" O MET B 529 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE B 500 " --> pdb=" O ASP B 567 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU B 569 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TRP B 502 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASN B 571 " --> pdb=" O TRP B 502 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR B 593 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ASN B 571 " --> pdb=" O THR B 593 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA B 595 " --> pdb=" O ASN B 571 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 739 through 744 removed outlier: 7.820A pdb=" N TYR B 659 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY B 684 " --> pdb=" O TYR B 659 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER B 661 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA B 686 " --> pdb=" O SER B 661 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 3 through 5 removed outlier: 5.371A pdb=" N ASP C 222 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE C 197 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N THR C 198 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 32 through 34 Processing sheet with id= S, first strand: chain 'C' and resid 93 through 95 Processing sheet with id= T, first strand: chain 'C' and resid 205 through 207 Processing sheet with id= U, first strand: chain 'C' and resid 263 through 268 Processing sheet with id= V, first strand: chain 'C' and resid 275 through 278 removed outlier: 6.308A pdb=" N ILE C 337 " --> pdb=" O TRP C 276 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N MET C 278 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE C 339 " --> pdb=" O MET C 278 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 537 through 543 removed outlier: 8.576A pdb=" N ALA C 527 " --> pdb=" O LEU C 549 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ALA C 499 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N MET C 529 " --> pdb=" O ALA C 499 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL C 501 " --> pdb=" O MET C 529 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE C 500 " --> pdb=" O ASP C 567 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU C 569 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TRP C 502 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ASN C 571 " --> pdb=" O TRP C 502 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR C 593 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ASN C 571 " --> pdb=" O THR C 593 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA C 595 " --> pdb=" O ASN C 571 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 739 through 745 removed outlier: 7.774A pdb=" N TYR C 659 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY C 684 " --> pdb=" O TYR C 659 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N SER C 661 " --> pdb=" O GLY C 684 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA C 686 " --> pdb=" O SER C 661 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 3 through 5 removed outlier: 5.528A pdb=" N ASP D 222 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE D 197 " --> pdb=" O ASP D 222 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N THR D 198 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 31 through 34 Processing sheet with id= AA, first strand: chain 'D' and resid 92 through 95 Processing sheet with id= AB, first strand: chain 'D' and resid 205 through 207 Processing sheet with id= AC, first strand: chain 'D' and resid 263 through 268 Processing sheet with id= AD, first strand: chain 'D' and resid 275 through 277 removed outlier: 6.329A pdb=" N ILE D 337 " --> pdb=" O TRP D 276 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 537 through 543 removed outlier: 8.544A pdb=" N ALA D 527 " --> pdb=" O LEU D 549 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ALA D 499 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N MET D 529 " --> pdb=" O ALA D 499 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL D 501 " --> pdb=" O MET D 529 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP D 567 " --> pdb=" O LYS D 498 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE D 500 " --> pdb=" O ASP D 567 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU D 569 " --> pdb=" O ILE D 500 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP D 502 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASN D 571 " --> pdb=" O TRP D 502 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR D 593 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ASN D 571 " --> pdb=" O THR D 593 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA D 595 " --> pdb=" O ASN D 571 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR D 619 " --> pdb=" O ILE D 594 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE D 596 " --> pdb=" O THR D 619 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE D 621 " --> pdb=" O ILE D 596 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 739 through 745 removed outlier: 7.829A pdb=" N TYR D 659 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY D 684 " --> pdb=" O TYR D 659 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N SER D 661 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA D 686 " --> pdb=" O SER D 661 " (cutoff:3.500A) 1171 hydrogen bonds defined for protein. 3333 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: 12.99 Time building geometry restraints manager: 13.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5306 1.29 - 1.43: 8077 1.43 - 1.56: 18924 1.56 - 1.69: 42 1.69 - 1.82: 296 Bond restraints: 32645 Sorted by residual: bond pdb=" C1B ACO A1201 " pdb=" C2B ACO A1201 " ideal model delta sigma weight residual 1.531 1.307 0.224 1.20e-02 6.94e+03 3.48e+02 bond pdb=" C1B ACO B1201 " pdb=" C2B ACO B1201 " ideal model delta sigma weight residual 1.531 1.308 0.223 1.20e-02 6.94e+03 3.45e+02 bond pdb=" C1B ACO D1201 " pdb=" C2B ACO D1201 " ideal model delta sigma weight residual 1.531 1.310 0.221 1.20e-02 6.94e+03 3.40e+02 bond pdb=" C1B ACO D1201 " pdb=" O4B ACO D1201 " ideal model delta sigma weight residual 1.416 1.642 -0.226 1.40e-02 5.10e+03 2.60e+02 bond pdb=" C1B ACO B1201 " pdb=" O4B ACO B1201 " ideal model delta sigma weight residual 1.416 1.640 -0.224 1.40e-02 5.10e+03 2.57e+02 ... (remaining 32640 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.89: 884 105.89 - 113.47: 17952 113.47 - 121.06: 16308 121.06 - 128.64: 8874 128.64 - 136.23: 217 Bond angle restraints: 44235 Sorted by residual: angle pdb=" P1ABACO A1202 " pdb=" O3ABACO A1202 " pdb=" P2ABACO A1202 " ideal model delta sigma weight residual 136.83 120.70 16.13 1.00e+00 1.00e+00 2.60e+02 angle pdb=" P1AAACO A1202 " pdb=" O3AAACO A1202 " pdb=" P2AAACO A1202 " ideal model delta sigma weight residual 136.83 122.22 14.61 1.00e+00 1.00e+00 2.13e+02 angle pdb=" P1A ACO A1201 " pdb=" O3A ACO A1201 " pdb=" P2A ACO A1201 " ideal model delta sigma weight residual 136.83 123.16 13.67 1.00e+00 1.00e+00 1.87e+02 angle pdb=" P1A ACO B1201 " pdb=" O3A ACO B1201 " pdb=" P2A ACO B1201 " ideal model delta sigma weight residual 136.83 123.39 13.44 1.00e+00 1.00e+00 1.81e+02 angle pdb=" N1A ACO B1201 " pdb=" C6A ACO B1201 " pdb=" N6A ACO B1201 " ideal model delta sigma weight residual 118.11 103.13 14.98 1.23e+00 6.64e-01 1.49e+02 ... (remaining 44230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.57: 18061 22.57 - 45.13: 1349 45.13 - 67.70: 145 67.70 - 90.27: 48 90.27 - 112.83: 1 Dihedral angle restraints: 19604 sinusoidal: 7964 harmonic: 11640 Sorted by residual: dihedral pdb=" CA GLY A 967 " pdb=" C GLY A 967 " pdb=" N LYS A 968 " pdb=" CA LYS A 968 " ideal model delta harmonic sigma weight residual 180.00 151.79 28.21 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA ARG D 835 " pdb=" C ARG D 835 " pdb=" N LYS D 836 " pdb=" CA LYS D 836 " ideal model delta harmonic sigma weight residual 180.00 152.50 27.50 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA TYR C 854 " pdb=" C TYR C 854 " pdb=" N ALA C 855 " pdb=" CA ALA C 855 " ideal model delta harmonic sigma weight residual -180.00 -153.26 -26.74 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 19601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3927 0.073 - 0.147: 870 0.147 - 0.220: 90 0.220 - 0.293: 15 0.293 - 0.367: 15 Chirality restraints: 4917 Sorted by residual: chirality pdb=" CA THR C 842 " pdb=" N THR C 842 " pdb=" C THR C 842 " pdb=" CB THR C 842 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA THR A 842 " pdb=" N THR A 842 " pdb=" C THR A 842 " pdb=" CB THR A 842 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA THR B 842 " pdb=" N THR B 842 " pdb=" C THR B 842 " pdb=" CB THR B 842 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 4914 not shown) Planarity restraints: 5656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7PAACO A1202 " -0.331 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C9PAACO A1202 " 0.077 2.00e-02 2.50e+03 pdb=" CAPAACO A1202 " -0.031 2.00e-02 2.50e+03 pdb=" N8PAACO A1202 " 0.496 2.00e-02 2.50e+03 pdb=" O9PAACO A1202 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3PAACO A1202 " 0.181 2.00e-02 2.50e+03 1.53e-01 2.92e+02 pdb=" C5PAACO A1202 " -0.039 2.00e-02 2.50e+03 pdb=" C6PAACO A1202 " -0.039 2.00e-02 2.50e+03 pdb=" N4PAACO A1202 " -0.246 2.00e-02 2.50e+03 pdb=" O5PAACO A1202 " 0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 854 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C TYR C 854 " 0.064 2.00e-02 2.50e+03 pdb=" O TYR C 854 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA C 855 " -0.022 2.00e-02 2.50e+03 ... (remaining 5653 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3109 2.74 - 3.28: 30266 3.28 - 3.82: 53455 3.82 - 4.36: 64439 4.36 - 4.90: 110405 Nonbonded interactions: 261674 Sorted by model distance: nonbonded pdb=" CD1 LEU B 833 " pdb=" O HOH B1301 " model vdw 2.199 3.460 nonbonded pdb=" O VAL C 394 " pdb=" OG1 THR C 398 " model vdw 2.234 2.440 nonbonded pdb=" O ALA A 578 " pdb=" OG1 THR A 582 " model vdw 2.249 2.440 nonbonded pdb=" O ALA B 578 " pdb=" OG1 THR B 582 " model vdw 2.261 2.440 nonbonded pdb=" O TRP A 49 " pdb=" OG SER A 52 " model vdw 2.263 2.440 ... (remaining 261669 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'B' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'C' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'D' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 4.540 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 105.880 Find NCS groups from input model: 2.760 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 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 : 0.010 0.226 32645 Z= 0.629 Angle : 1.063 16.134 44235 Z= 0.620 Chirality : 0.063 0.367 4917 Planarity : 0.009 0.285 5656 Dihedral : 15.416 112.833 12212 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.45 % Favored : 93.35 % Rotamer: Outliers : 0.50 % Allowed : 7.36 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.10), residues: 4068 helix: -3.08 (0.08), residues: 1726 sheet: -1.62 (0.20), residues: 582 loop : -2.73 (0.12), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 84 HIS 0.017 0.002 HIS C 47 PHE 0.024 0.002 PHE A 998 TYR 0.039 0.003 TYR C 319 ARG 0.032 0.001 ARG B 848 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 489 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.8337 (m-80) cc_final: 0.7769 (m-80) REVERT: A 667 SER cc_start: 0.8008 (p) cc_final: 0.7248 (p) REVERT: A 671 ASN cc_start: 0.8438 (m-40) cc_final: 0.8173 (m-40) REVERT: A 992 ASP cc_start: 0.7624 (m-30) cc_final: 0.7182 (m-30) REVERT: A 1035 ASP cc_start: 0.7711 (t0) cc_final: 0.7425 (t0) REVERT: A 1036 MET cc_start: 0.8486 (tmm) cc_final: 0.8272 (ttp) REVERT: A 1090 ASP cc_start: 0.8238 (t70) cc_final: 0.7811 (t0) REVERT: B 642 MET cc_start: 0.8660 (ttm) cc_final: 0.8413 (ttm) REVERT: B 666 MET cc_start: 0.7481 (mmm) cc_final: 0.7265 (mmt) REVERT: B 965 LYS cc_start: 0.8868 (mtmt) cc_final: 0.8087 (mmtp) REVERT: B 996 GLN cc_start: 0.8367 (mt0) cc_final: 0.8149 (mt0) REVERT: B 1080 LYS cc_start: 0.8733 (mttt) cc_final: 0.8513 (mttm) REVERT: B 1090 ASP cc_start: 0.8360 (t70) cc_final: 0.8068 (t0) REVERT: C 1090 ASP cc_start: 0.8524 (t70) cc_final: 0.8290 (t0) outliers start: 14 outliers final: 7 residues processed: 499 average time/residue: 0.4754 time to fit residues: 367.6311 Evaluate side-chains 361 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 354 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 952 SER Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain C residue 620 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 20.0000 chunk 309 optimal weight: 50.0000 chunk 171 optimal weight: 0.6980 chunk 105 optimal weight: 40.0000 chunk 208 optimal weight: 50.0000 chunk 165 optimal weight: 5.9990 chunk 319 optimal weight: 40.0000 chunk 123 optimal weight: 20.0000 chunk 194 optimal weight: 0.8980 chunk 238 optimal weight: 20.0000 chunk 370 optimal weight: 3.9990 overall best weight: 6.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 75 ASN A 104 ASN ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN A 410 HIS ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 GLN A 900 HIS A 908 HIS A 961 ASN A1024 ASN A1086 HIS B 27 ASN B 61 GLN B 299 ASN B 314 GLN B 315 GLN ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 HIS B 961 ASN B1024 ASN C 9 GLN C 47 HIS C 270 ASN ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 421 HIS C 645 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 GLN C 879 GLN C 900 HIS C 908 HIS C 909 ASN C 982 ASN C 997 HIS C1024 ASN D 61 GLN D 168 HIS D 190 ASN D 203 ASN D 270 ASN D 299 ASN D 315 GLN D 403 HIS D 638 ASN D 671 ASN ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 908 HIS D 961 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 32645 Z= 0.426 Angle : 0.697 9.445 44235 Z= 0.359 Chirality : 0.049 0.229 4917 Planarity : 0.006 0.088 5656 Dihedral : 9.067 109.049 4727 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.66 % Allowed : 12.83 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.12), residues: 4068 helix: -1.69 (0.11), residues: 1732 sheet: -1.49 (0.21), residues: 565 loop : -2.47 (0.13), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 84 HIS 0.007 0.001 HIS C 47 PHE 0.020 0.002 PHE C 998 TYR 0.036 0.002 TYR C 319 ARG 0.009 0.001 ARG D 676 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 355 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 992 ASP cc_start: 0.7187 (m-30) cc_final: 0.6939 (m-30) REVERT: A 1035 ASP cc_start: 0.7674 (t0) cc_final: 0.7462 (t0) REVERT: A 1090 ASP cc_start: 0.8375 (t70) cc_final: 0.7904 (t0) REVERT: B 998 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.6872 (t80) REVERT: B 1080 LYS cc_start: 0.8764 (mttt) cc_final: 0.8520 (mttm) REVERT: B 1090 ASP cc_start: 0.8564 (t70) cc_final: 0.8148 (t0) REVERT: C 1090 ASP cc_start: 0.8617 (t70) cc_final: 0.8372 (t0) REVERT: D 996 GLN cc_start: 0.8072 (mt0) cc_final: 0.7862 (mt0) outliers start: 53 outliers final: 35 residues processed: 392 average time/residue: 0.4168 time to fit residues: 266.4189 Evaluate side-chains 371 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 335 time to evaluate : 3.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 843 SER Chi-restraints excluded: chain D residue 844 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 20.0000 chunk 114 optimal weight: 30.0000 chunk 308 optimal weight: 0.9980 chunk 252 optimal weight: 10.0000 chunk 102 optimal weight: 30.0000 chunk 371 optimal weight: 20.0000 chunk 400 optimal weight: 1.9990 chunk 330 optimal weight: 20.0000 chunk 368 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 297 optimal weight: 0.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN B 53 GLN B 314 GLN ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN D 9 GLN D 168 HIS ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 32645 Z= 0.453 Angle : 0.693 9.920 44235 Z= 0.355 Chirality : 0.049 0.238 4917 Planarity : 0.005 0.089 5656 Dihedral : 8.678 106.343 4720 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.40 % Allowed : 14.40 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.12), residues: 4068 helix: -1.14 (0.12), residues: 1761 sheet: -1.37 (0.21), residues: 589 loop : -2.30 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 84 HIS 0.007 0.001 HIS A1086 PHE 0.029 0.002 PHE A 347 TYR 0.029 0.002 TYR C 319 ARG 0.008 0.001 ARG D 848 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 344 time to evaluate : 3.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 666 MET cc_start: 0.7840 (mmm) cc_final: 0.7455 (mmm) REVERT: A 671 ASN cc_start: 0.8599 (m110) cc_final: 0.8312 (m110) REVERT: A 690 ASP cc_start: 0.6936 (p0) cc_final: 0.6625 (p0) REVERT: A 985 MET cc_start: 0.7504 (tpp) cc_final: 0.7095 (tpt) REVERT: A 1001 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.7903 (t) REVERT: A 1035 ASP cc_start: 0.7718 (t0) cc_final: 0.7482 (t0) REVERT: A 1090 ASP cc_start: 0.8470 (t70) cc_final: 0.8000 (t0) REVERT: B 835 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8037 (ptm160) REVERT: B 998 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.6902 (t80) REVERT: B 1080 LYS cc_start: 0.8776 (mttt) cc_final: 0.8536 (mttm) REVERT: B 1090 ASP cc_start: 0.8651 (t70) cc_final: 0.8239 (t0) REVERT: C 1090 ASP cc_start: 0.8620 (t70) cc_final: 0.8409 (t0) outliers start: 77 outliers final: 52 residues processed: 398 average time/residue: 0.4355 time to fit residues: 286.3526 Evaluate side-chains 385 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 330 time to evaluate : 3.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 820 THR Chi-restraints excluded: chain B residue 823 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 542 TYR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 841 MET Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 9.9990 chunk 279 optimal weight: 5.9990 chunk 192 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 249 optimal weight: 4.9990 chunk 372 optimal weight: 9.9990 chunk 394 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 353 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN B 314 GLN ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 HIS ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 961 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32645 Z= 0.245 Angle : 0.597 13.712 44235 Z= 0.304 Chirality : 0.045 0.243 4917 Planarity : 0.004 0.082 5656 Dihedral : 8.110 103.392 4720 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.14 % Allowed : 16.15 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.13), residues: 4068 helix: -0.66 (0.12), residues: 1765 sheet: -1.23 (0.21), residues: 583 loop : -2.08 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 84 HIS 0.005 0.001 HIS C1086 PHE 0.024 0.001 PHE A 347 TYR 0.026 0.001 TYR A 304 ARG 0.005 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 352 time to evaluate : 3.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8351 (tp) REVERT: A 985 MET cc_start: 0.7533 (tpp) cc_final: 0.7258 (tpt) REVERT: A 1001 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.7750 (t) REVERT: A 1035 ASP cc_start: 0.7630 (t0) cc_final: 0.7368 (t0) REVERT: A 1090 ASP cc_start: 0.8390 (t70) cc_final: 0.7925 (t0) REVERT: B 504 MET cc_start: 0.8453 (tpp) cc_final: 0.8158 (mpp) REVERT: B 998 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.6847 (t80) REVERT: B 1090 ASP cc_start: 0.8441 (t70) cc_final: 0.8126 (t0) REVERT: C 504 MET cc_start: 0.8496 (tpp) cc_final: 0.8266 (mmm) REVERT: D 411 MET cc_start: 0.6872 (ttp) cc_final: 0.6423 (ptm) REVERT: D 888 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7283 (tp40) outliers start: 68 outliers final: 46 residues processed: 398 average time/residue: 0.4227 time to fit residues: 276.9340 Evaluate side-chains 384 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 334 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 823 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 542 TYR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 839 SER Chi-restraints excluded: chain C residue 841 MET Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 888 GLN Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 0.0370 chunk 223 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 chunk 293 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 336 optimal weight: 8.9990 chunk 272 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 201 optimal weight: 0.9980 chunk 353 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 overall best weight: 3.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 HIS B 988 GLN ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 GLN C 421 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32645 Z= 0.239 Angle : 0.588 12.981 44235 Z= 0.298 Chirality : 0.045 0.216 4917 Planarity : 0.004 0.079 5656 Dihedral : 7.832 99.215 4720 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.67 % Allowed : 16.24 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 (0.13), residues: 4068 helix: -0.44 (0.12), residues: 1772 sheet: -1.07 (0.21), residues: 591 loop : -1.97 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 84 HIS 0.007 0.001 HIS B 545 PHE 0.021 0.001 PHE A 347 TYR 0.024 0.001 TYR A 304 ARG 0.005 0.000 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 345 time to evaluate : 3.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 690 ASP cc_start: 0.6883 (p0) cc_final: 0.6668 (p0) REVERT: A 1001 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.7730 (t) REVERT: A 1035 ASP cc_start: 0.7598 (t0) cc_final: 0.7338 (t0) REVERT: A 1046 GLU cc_start: 0.7190 (tp30) cc_final: 0.6958 (tp30) REVERT: A 1090 ASP cc_start: 0.8379 (t70) cc_final: 0.7934 (t0) REVERT: B 504 MET cc_start: 0.8427 (tpp) cc_final: 0.8194 (mpp) REVERT: B 560 MET cc_start: 0.8194 (mmt) cc_final: 0.7873 (mmt) REVERT: B 933 ASP cc_start: 0.6842 (OUTLIER) cc_final: 0.6585 (p0) REVERT: B 998 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.6939 (t80) REVERT: B 1090 ASP cc_start: 0.8412 (t70) cc_final: 0.8093 (t0) REVERT: C 998 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6908 (t80) REVERT: D 411 MET cc_start: 0.6795 (ttp) cc_final: 0.6352 (ptm) REVERT: D 888 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7291 (tp40) outliers start: 86 outliers final: 62 residues processed: 406 average time/residue: 0.4219 time to fit residues: 280.4161 Evaluate side-chains 397 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 330 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 820 THR Chi-restraints excluded: chain B residue 823 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1067 MET Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 542 TYR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 839 SER Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 998 PHE Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 843 SER Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 888 GLN Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 30.0000 chunk 355 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 231 optimal weight: 50.0000 chunk 97 optimal weight: 0.9980 chunk 394 optimal weight: 6.9990 chunk 327 optimal weight: 7.9990 chunk 182 optimal weight: 0.9990 chunk 32 optimal weight: 30.0000 chunk 130 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS D 410 HIS D 672 ASN ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 32645 Z= 0.326 Angle : 0.614 9.903 44235 Z= 0.312 Chirality : 0.047 0.241 4917 Planarity : 0.005 0.080 5656 Dihedral : 7.821 95.934 4720 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.82 % Allowed : 16.86 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.74 (0.13), residues: 4068 helix: -0.39 (0.12), residues: 1778 sheet: -1.08 (0.21), residues: 609 loop : -1.94 (0.14), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 49 HIS 0.006 0.001 HIS A1086 PHE 0.020 0.002 PHE A 347 TYR 0.023 0.002 TYR C 319 ARG 0.013 0.000 ARG D 676 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 326 time to evaluate : 3.364 Fit side-chains revert: symmetry clash REVERT: A 690 ASP cc_start: 0.6904 (p0) cc_final: 0.6622 (p0) REVERT: A 831 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8345 (pp) REVERT: A 963 MET cc_start: 0.8392 (mmp) cc_final: 0.8108 (mmm) REVERT: A 1001 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.7803 (t) REVERT: A 1035 ASP cc_start: 0.7604 (t0) cc_final: 0.7346 (t0) REVERT: A 1046 GLU cc_start: 0.7254 (tp30) cc_final: 0.6980 (tp30) REVERT: A 1090 ASP cc_start: 0.8428 (t70) cc_final: 0.7985 (t0) REVERT: B 364 TYR cc_start: 0.6231 (OUTLIER) cc_final: 0.5942 (m-10) REVERT: B 835 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8020 (ptm160) REVERT: B 933 ASP cc_start: 0.6960 (OUTLIER) cc_final: 0.6691 (p0) REVERT: B 998 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.6884 (t80) REVERT: B 1090 ASP cc_start: 0.8465 (t70) cc_final: 0.8145 (t0) REVERT: D 411 MET cc_start: 0.6900 (ttp) cc_final: 0.6479 (ptm) REVERT: D 888 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7391 (tp40) outliers start: 91 outliers final: 72 residues processed: 394 average time/residue: 0.4074 time to fit residues: 266.0608 Evaluate side-chains 398 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 319 time to evaluate : 3.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 820 THR Chi-restraints excluded: chain B residue 823 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 542 TYR Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 839 SER Chi-restraints excluded: chain C residue 841 MET Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 940 ASP Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 843 SER Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 888 GLN Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.0270 chunk 44 optimal weight: 4.9990 chunk 224 optimal weight: 50.0000 chunk 288 optimal weight: 4.9990 chunk 223 optimal weight: 8.9990 chunk 332 optimal weight: 30.0000 chunk 220 optimal weight: 5.9990 chunk 393 optimal weight: 2.9990 chunk 246 optimal weight: 20.0000 chunk 239 optimal weight: 8.9990 chunk 181 optimal weight: 0.8980 overall best weight: 2.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS D 900 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32645 Z= 0.228 Angle : 0.583 13.725 44235 Z= 0.294 Chirality : 0.045 0.278 4917 Planarity : 0.004 0.078 5656 Dihedral : 7.576 94.151 4720 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.76 % Allowed : 17.40 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.53 (0.13), residues: 4068 helix: -0.22 (0.12), residues: 1776 sheet: -0.89 (0.21), residues: 589 loop : -1.85 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 84 HIS 0.005 0.001 HIS C1086 PHE 0.023 0.001 PHE A 347 TYR 0.023 0.001 TYR A 304 ARG 0.011 0.000 ARG D 676 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 332 time to evaluate : 3.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 831 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8277 (pp) REVERT: A 963 MET cc_start: 0.8373 (mmp) cc_final: 0.8081 (mmm) REVERT: A 985 MET cc_start: 0.7534 (tpp) cc_final: 0.7220 (tpt) REVERT: A 1001 THR cc_start: 0.8383 (OUTLIER) cc_final: 0.7722 (t) REVERT: A 1035 ASP cc_start: 0.7551 (t0) cc_final: 0.7287 (t0) REVERT: A 1046 GLU cc_start: 0.7183 (tp30) cc_final: 0.6933 (tp30) REVERT: A 1090 ASP cc_start: 0.8373 (t70) cc_final: 0.7933 (t0) REVERT: B 835 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.7321 (ptm160) REVERT: B 933 ASP cc_start: 0.6808 (OUTLIER) cc_final: 0.6570 (p0) REVERT: B 998 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.6898 (t80) REVERT: B 1090 ASP cc_start: 0.8348 (t70) cc_final: 0.8095 (t0) REVERT: C 998 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6883 (t80) REVERT: D 411 MET cc_start: 0.6865 (ttp) cc_final: 0.6451 (ptm) REVERT: D 888 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7278 (tp40) outliers start: 89 outliers final: 72 residues processed: 398 average time/residue: 0.4154 time to fit residues: 272.2239 Evaluate side-chains 399 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 320 time to evaluate : 3.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 820 THR Chi-restraints excluded: chain B residue 823 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 652 TYR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 706 ASP Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 839 SER Chi-restraints excluded: chain C residue 841 MET Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 940 ASP Chi-restraints excluded: chain C residue 998 PHE Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 843 SER Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 888 GLN Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 234 optimal weight: 50.0000 chunk 118 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 250 optimal weight: 7.9990 chunk 267 optimal weight: 20.0000 chunk 194 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 309 optimal weight: 3.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 ASN ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 32645 Z= 0.322 Angle : 0.615 12.762 44235 Z= 0.310 Chirality : 0.047 0.277 4917 Planarity : 0.004 0.079 5656 Dihedral : 7.611 92.380 4720 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.85 % Allowed : 17.58 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.53 (0.13), residues: 4068 helix: -0.21 (0.12), residues: 1769 sheet: -0.89 (0.21), residues: 616 loop : -1.88 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 84 HIS 0.006 0.001 HIS A1086 PHE 0.029 0.002 PHE A 347 TYR 0.021 0.002 TYR A 304 ARG 0.010 0.000 ARG D 676 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 328 time to evaluate : 3.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 831 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8326 (pp) REVERT: A 1001 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.7790 (t) REVERT: A 1035 ASP cc_start: 0.7618 (t0) cc_final: 0.7356 (t0) REVERT: A 1046 GLU cc_start: 0.7247 (tp30) cc_final: 0.6985 (tp30) REVERT: A 1090 ASP cc_start: 0.8427 (t70) cc_final: 0.7955 (t0) REVERT: B 364 TYR cc_start: 0.6133 (OUTLIER) cc_final: 0.5745 (m-10) REVERT: B 504 MET cc_start: 0.8452 (tpp) cc_final: 0.8165 (mpp) REVERT: B 560 MET cc_start: 0.8252 (mmt) cc_final: 0.7966 (mmt) REVERT: B 835 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8105 (ptm160) REVERT: B 848 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.6843 (pmt-80) REVERT: B 933 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6681 (p0) REVERT: B 998 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.6971 (t80) REVERT: B 1090 ASP cc_start: 0.8430 (t70) cc_final: 0.8127 (t0) REVERT: D 411 MET cc_start: 0.6940 (ttp) cc_final: 0.6583 (ptm) REVERT: D 888 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7334 (tp40) outliers start: 92 outliers final: 74 residues processed: 395 average time/residue: 0.4074 time to fit residues: 266.5734 Evaluate side-chains 401 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 319 time to evaluate : 3.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 820 THR Chi-restraints excluded: chain B residue 823 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 542 TYR Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 652 TYR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 839 SER Chi-restraints excluded: chain C residue 841 MET Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 940 ASP Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 843 SER Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 888 GLN Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 3.9990 chunk 376 optimal weight: 0.3980 chunk 343 optimal weight: 20.0000 chunk 366 optimal weight: 10.0000 chunk 220 optimal weight: 20.0000 chunk 159 optimal weight: 4.9990 chunk 287 optimal weight: 0.9980 chunk 112 optimal weight: 30.0000 chunk 331 optimal weight: 9.9990 chunk 346 optimal weight: 10.0000 chunk 365 optimal weight: 7.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32645 Z= 0.275 Angle : 0.602 13.182 44235 Z= 0.303 Chirality : 0.046 0.239 4917 Planarity : 0.004 0.078 5656 Dihedral : 7.499 93.320 4720 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.73 % Allowed : 17.90 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.41 (0.13), residues: 4068 helix: -0.10 (0.13), residues: 1758 sheet: -0.84 (0.21), residues: 589 loop : -1.79 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 84 HIS 0.005 0.001 HIS C1086 PHE 0.014 0.001 PHE C 998 TYR 0.024 0.001 TYR C 319 ARG 0.010 0.000 ARG D 676 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 324 time to evaluate : 3.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 MET cc_start: 0.7544 (tpp) cc_final: 0.7318 (ttm) REVERT: A 831 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8311 (pp) REVERT: A 1001 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.7772 (t) REVERT: A 1035 ASP cc_start: 0.7598 (t0) cc_final: 0.7332 (t0) REVERT: A 1046 GLU cc_start: 0.7181 (tp30) cc_final: 0.6923 (tp30) REVERT: A 1090 ASP cc_start: 0.8402 (t70) cc_final: 0.7946 (t0) REVERT: B 364 TYR cc_start: 0.6128 (OUTLIER) cc_final: 0.5694 (m-10) REVERT: B 504 MET cc_start: 0.8425 (tpp) cc_final: 0.8182 (mpp) REVERT: B 560 MET cc_start: 0.8270 (mmt) cc_final: 0.7976 (mmt) REVERT: B 835 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8134 (ptm160) REVERT: B 848 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.6672 (pmt-80) REVERT: B 933 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6621 (p0) REVERT: B 998 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.6951 (t80) REVERT: B 1090 ASP cc_start: 0.8375 (t70) cc_final: 0.8091 (t0) REVERT: D 411 MET cc_start: 0.6981 (ttp) cc_final: 0.6561 (ptm) REVERT: D 888 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.7316 (tp40) REVERT: D 1090 ASP cc_start: 0.8077 (t0) cc_final: 0.7522 (t0) outliers start: 88 outliers final: 76 residues processed: 388 average time/residue: 0.4138 time to fit residues: 266.0414 Evaluate side-chains 408 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 324 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 820 THR Chi-restraints excluded: chain B residue 823 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 971 MET Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 542 TYR Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 652 TYR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 839 SER Chi-restraints excluded: chain C residue 841 MET Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 940 ASP Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 843 SER Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 888 GLN Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 20.0000 chunk 387 optimal weight: 1.9990 chunk 236 optimal weight: 0.0050 chunk 183 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 chunk 406 optimal weight: 0.9980 chunk 374 optimal weight: 0.0970 chunk 323 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 250 optimal weight: 0.0040 chunk 198 optimal weight: 3.9990 overall best weight: 0.4206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 ASN B 314 GLN B 982 ASN C 9 GLN ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 909 ASN D 168 HIS D 850 GLN D 961 ASN D 997 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 32645 Z= 0.144 Angle : 0.557 13.847 44235 Z= 0.281 Chirality : 0.044 0.253 4917 Planarity : 0.004 0.071 5656 Dihedral : 6.947 91.912 4720 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.72 % Allowed : 18.94 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.09 (0.13), residues: 4068 helix: 0.13 (0.13), residues: 1759 sheet: -0.69 (0.22), residues: 589 loop : -1.58 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 84 HIS 0.004 0.000 HIS B 410 PHE 0.015 0.001 PHE A 197 TYR 0.025 0.001 TYR A 304 ARG 0.010 0.000 ARG D 676 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 356 time to evaluate : 3.511 Fit side-chains revert: symmetry clash REVERT: A 831 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.7975 (pp) REVERT: A 985 MET cc_start: 0.7455 (tpp) cc_final: 0.7163 (tpt) REVERT: A 1001 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7468 (t) REVERT: A 1035 ASP cc_start: 0.7441 (t0) cc_final: 0.7183 (t0) REVERT: A 1046 GLU cc_start: 0.7129 (tp30) cc_final: 0.6914 (tp30) REVERT: A 1090 ASP cc_start: 0.8267 (t70) cc_final: 0.7858 (t0) REVERT: B 560 MET cc_start: 0.8214 (mmt) cc_final: 0.7877 (mmt) REVERT: B 835 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.7953 (ptm160) REVERT: C 1011 GLU cc_start: 0.8153 (tt0) cc_final: 0.7950 (tt0) REVERT: D 888 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.7148 (tp40) outliers start: 54 outliers final: 42 residues processed: 396 average time/residue: 0.4112 time to fit residues: 268.6648 Evaluate side-chains 375 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 329 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 652 TYR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 888 GLN Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 20.0000 chunk 344 optimal weight: 0.0270 chunk 99 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 324 optimal weight: 20.0000 chunk 135 optimal weight: 6.9990 chunk 332 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 HIS ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 909 ASN D 168 HIS D 672 ASN ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.189383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.163182 restraints weight = 88247.540| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.52 r_work: 0.3727 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32645 Z= 0.270 Angle : 0.593 13.282 44235 Z= 0.298 Chirality : 0.046 0.223 4917 Planarity : 0.004 0.082 5656 Dihedral : 7.044 87.955 4720 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.66 % Allowed : 19.30 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.11 (0.13), residues: 4068 helix: 0.10 (0.13), residues: 1760 sheet: -0.71 (0.22), residues: 591 loop : -1.58 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 84 HIS 0.005 0.001 HIS A1086 PHE 0.014 0.001 PHE B 998 TYR 0.022 0.001 TYR D 124 ARG 0.010 0.000 ARG D 676 =============================================================================== Job complete usr+sys time: 7244.39 seconds wall clock time: 132 minutes 29.37 seconds (7949.37 seconds total)