Starting phenix.real_space_refine on Sat Feb 17 16:18:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn4_22267/02_2024/6xn4_22267.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn4_22267/02_2024/6xn4_22267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn4_22267/02_2024/6xn4_22267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn4_22267/02_2024/6xn4_22267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn4_22267/02_2024/6xn4_22267.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn4_22267/02_2024/6xn4_22267.pdb" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 64 5.49 5 S 48 5.16 5 C 12041 2.51 5 N 3263 2.21 5 O 3857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 9": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "F GLU 120": "OE1" <-> "OE2" Residue "H TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 210": "OE1" <-> "OE2" Residue "G GLU 136": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "D PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 35": "NH1" <-> "NH2" Residue "D ARG 70": "NH1" <-> "NH2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A ARG 740": "NH1" <-> "NH2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "J ARG 6": "NH1" <-> "NH2" Residue "J GLU 51": "OE1" <-> "OE2" Residue "J ARG 61": "NH1" <-> "NH2" Residue "J ARG 123": "NH1" <-> "NH2" Residue "J GLU 149": "OE1" <-> "OE2" Residue "J GLU 196": "OE1" <-> "OE2" Residue "J ARG 288": "NH1" <-> "NH2" Residue "J ARG 304": "NH1" <-> "NH2" Residue "J ARG 311": "NH1" <-> "NH2" Residue "J ARG 346": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19273 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 2227 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 275, 2225 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 263} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 275, 2225 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 263} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2272 Chain: "F" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1617 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 4, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 207} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "R" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 736 Classifications: {'RNA': 35} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 6, 'rna3p_pur': 7, 'rna3p_pyr': 12} Link IDs: {'rna2p': 16, 'rna3p': 18} Chain: "C" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1115 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain: "D" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1089 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "T" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 644 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 25} Chain: "A" Number of atoms: 5984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5984 Classifications: {'peptide': 741} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 730} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2515 Classifications: {'peptide': 309} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 11, 'TRANS': 294} Chain breaks: 3 Time building chain proxies: 11.46, per 1000 atoms: 0.59 Number of scatterers: 19273 At special positions: 0 Unit cell: (109.548, 126.732, 183.654, 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 48 16.00 P 64 15.00 O 3857 8.00 N 3263 7.00 C 12041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 421 " distance=2.01 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 421 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.89 Conformation dependent library (CDL) restraints added in 3.5 seconds 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4184 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 24 sheets defined 40.5% alpha, 12.8% beta 2 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 6.34 Creating SS restraints... Processing helix chain 'B' and resid 27 through 43 Processing helix chain 'B' and resid 44 through 54 Processing helix chain 'B' and resid 163 through 171 removed outlier: 3.582A pdb=" N GLU B 171 " --> pdb=" O GLU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.555A pdb=" N PHE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 227 removed outlier: 4.073A pdb=" N LEU B 227 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 61 removed outlier: 3.543A pdb=" N LEU F 49 " --> pdb=" O PRO F 45 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 80 Processing helix chain 'F' and resid 154 through 156 No H-bonds generated for 'chain 'F' and resid 154 through 156' Processing helix chain 'F' and resid 157 through 172 removed outlier: 3.600A pdb=" N GLY F 168 " --> pdb=" O ASN F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 184 removed outlier: 3.546A pdb=" N ARG F 183 " --> pdb=" O HIS F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 214 Processing helix chain 'H' and resid 45 through 61 Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 157 through 174 removed outlier: 3.537A pdb=" N ASN H 164 " --> pdb=" O LYS H 160 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS H 166 " --> pdb=" O PHE H 162 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE H 174 " --> pdb=" O ASP H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'G' and resid 45 through 61 removed outlier: 3.797A pdb=" N LEU G 49 " --> pdb=" O PRO G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 82 Processing helix chain 'G' and resid 103 through 110 Processing helix chain 'G' and resid 157 through 173 Processing helix chain 'G' and resid 204 through 213 Processing helix chain 'C' and resid 26 through 38 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.539A pdb=" N ILE C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ARG C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 101 removed outlier: 3.732A pdb=" N GLU C 101 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 111 Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'D' and resid 25 through 38 Processing helix chain 'D' and resid 53 through 73 removed outlier: 4.369A pdb=" N VAL D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN D 73 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 101 removed outlier: 3.554A pdb=" N ALA D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 111 removed outlier: 3.621A pdb=" N THR D 111 " --> pdb=" O PHE D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 125 through 146 removed outlier: 3.506A pdb=" N TYR D 146 " --> pdb=" O TYR D 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 11 Processing helix chain 'A' and resid 14 through 19 removed outlier: 3.657A pdb=" N LYS A 17 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 19 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 40 removed outlier: 4.300A pdb=" N LYS A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 72 through 85 removed outlier: 4.116A pdb=" N THR A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR A 77 " --> pdb=" O PHE A 73 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.801A pdb=" N LYS A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 168 removed outlier: 3.522A pdb=" N TYR A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLN A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.848A pdb=" N VAL A 199 " --> pdb=" O ASN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 224 removed outlier: 3.597A pdb=" N HIS A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 270 through 295 removed outlier: 4.081A pdb=" N ASP A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 337 Processing helix chain 'A' and resid 364 through 381 Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 418 through 430 removed outlier: 3.878A pdb=" N SER A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG A 429 " --> pdb=" O GLN A 425 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 removed outlier: 3.931A pdb=" N SER A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 505 removed outlier: 3.679A pdb=" N GLU A 505 " --> pdb=" O HIS A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 540 through 564 removed outlier: 3.920A pdb=" N THR A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 603 removed outlier: 4.391A pdb=" N ASP A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 638 removed outlier: 3.710A pdb=" N ASP A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 674 Processing helix chain 'A' and resid 674 through 682 removed outlier: 3.522A pdb=" N GLU A 682 " --> pdb=" O THR A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 701 removed outlier: 3.654A pdb=" N GLY A 701 " --> pdb=" O ASP A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 720 Processing helix chain 'A' and resid 727 through 739 Processing helix chain 'A' and resid 740 through 754 removed outlier: 3.574A pdb=" N MET A 745 " --> pdb=" O LYS A 741 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 746 " --> pdb=" O THR A 742 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.514A pdb=" N THR J 46 " --> pdb=" O HIS J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 65 removed outlier: 3.803A pdb=" N VAL J 62 " --> pdb=" O PHE J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 76 Processing helix chain 'J' and resid 127 through 138 removed outlier: 3.684A pdb=" N LEU J 131 " --> pdb=" O PRO J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 155 removed outlier: 3.637A pdb=" N ALA J 154 " --> pdb=" O GLU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 167 No H-bonds generated for 'chain 'J' and resid 165 through 167' Processing helix chain 'J' and resid 209 through 229 removed outlier: 3.650A pdb=" N ILE J 213 " --> pdb=" O THR J 209 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP J 228 " --> pdb=" O TYR J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 301 removed outlier: 4.047A pdb=" N GLN J 290 " --> pdb=" O LYS J 286 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG J 292 " --> pdb=" O ARG J 288 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU J 299 " --> pdb=" O SER J 295 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 97 through 99 removed outlier: 3.649A pdb=" N PHE B 65 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 7 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 123 through 132 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 265 Processing sheet with id=AA4, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AA5, first strand: chain 'B' and resid 274 through 277 removed outlier: 5.858A pdb=" N VAL B 284 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 94 through 96 removed outlier: 7.675A pdb=" N LYS F 2 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N THR F 8 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ASN F 192 " --> pdb=" O THR F 8 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL F 10 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE F 190 " --> pdb=" O VAL F 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AA8, first strand: chain 'F' and resid 115 through 123 Processing sheet with id=AA9, first strand: chain 'H' and resid 94 through 95 removed outlier: 3.723A pdb=" N PHE H 146 " --> pdb=" O GLY H 7 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR H 8 " --> pdb=" O ASN H 192 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ASN H 192 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL H 10 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N PHE H 190 " --> pdb=" O VAL H 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 43 through 44 Processing sheet with id=AB2, first strand: chain 'H' and resid 115 through 123 Processing sheet with id=AB3, first strand: chain 'G' and resid 94 through 95 removed outlier: 6.447A pdb=" N VAL G 4 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL G 195 " --> pdb=" O VAL G 4 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU G 6 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU G 193 " --> pdb=" O GLU G 6 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AB5, first strand: chain 'G' and resid 115 through 120 Processing sheet with id=AB6, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.804A pdb=" N PHE C 42 " --> pdb=" O GLN C 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 304 through 305 removed outlier: 4.215A pdb=" N PHE A 247 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 352 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 249 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR A 344 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 439 through 440 Processing sheet with id=AB9, first strand: chain 'A' and resid 473 through 475 Processing sheet with id=AC1, first strand: chain 'A' and resid 568 through 570 removed outlier: 3.518A pdb=" N ALA A 651 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 3 through 5 Processing sheet with id=AC3, first strand: chain 'J' and resid 196 through 198 Processing sheet with id=AC4, first strand: chain 'J' and resid 22 through 23 removed outlier: 6.666A pdb=" N LEU J 184 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASP J 176 " --> pdb=" O LEU J 184 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LEU J 186 " --> pdb=" O LYS J 174 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN J 173 " --> pdb=" O ALA J 91 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 37 through 40 removed outlier: 3.897A pdb=" N TYR J 86 " --> pdb=" O MET J 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 314 through 315 729 hydrogen bonds defined for protein. 2103 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 8 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 6.43 Time building geometry restraints manager: 8.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6115 1.34 - 1.48: 5333 1.48 - 1.62: 8202 1.62 - 1.76: 4 1.76 - 1.89: 88 Bond restraints: 19742 Sorted by residual: bond pdb=" CA ASN J 141 " pdb=" C ASN J 141 " ideal model delta sigma weight residual 1.522 1.436 0.087 1.37e-02 5.33e+03 4.00e+01 bond pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.15e-02 7.56e+03 1.28e+01 bond pdb=" C LYS J 170 " pdb=" N VAL J 171 " ideal model delta sigma weight residual 1.329 1.289 0.040 1.46e-02 4.69e+03 7.61e+00 bond pdb=" CG1 ILE A 708 " pdb=" CD1 ILE A 708 " ideal model delta sigma weight residual 1.513 1.407 0.106 3.90e-02 6.57e+02 7.45e+00 bond pdb=" C GLN J 259 " pdb=" N PRO J 260 " ideal model delta sigma weight residual 1.335 1.367 -0.032 1.19e-02 7.06e+03 7.37e+00 ... (remaining 19737 not shown) Histogram of bond angle deviations from ideal: 90.42 - 99.72: 17 99.72 - 109.02: 2162 109.02 - 118.32: 13267 118.32 - 127.62: 11222 127.62 - 136.92: 220 Bond angle restraints: 26888 Sorted by residual: angle pdb=" CA CYS A 418 " pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " ideal model delta sigma weight residual 114.40 134.77 -20.37 2.30e+00 1.89e-01 7.84e+01 angle pdb=" C SER H 20 " pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta sigma weight residual 123.91 136.92 -13.01 1.66e+00 3.63e-01 6.14e+01 angle pdb=" N ILE J 17 " pdb=" CA ILE J 17 " pdb=" C ILE J 17 " ideal model delta sigma weight residual 113.71 107.32 6.39 9.50e-01 1.11e+00 4.53e+01 angle pdb=" N ILE A 341 " pdb=" CA ILE A 341 " pdb=" C ILE A 341 " ideal model delta sigma weight residual 113.71 107.52 6.19 9.50e-01 1.11e+00 4.24e+01 angle pdb=" N VAL A 199 " pdb=" CA VAL A 199 " pdb=" C VAL A 199 " ideal model delta sigma weight residual 113.10 107.33 5.77 9.70e-01 1.06e+00 3.54e+01 ... (remaining 26883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.63: 11568 34.63 - 69.25: 374 69.25 - 103.88: 38 103.88 - 138.50: 4 138.50 - 173.13: 2 Dihedral angle restraints: 11986 sinusoidal: 5486 harmonic: 6500 Sorted by residual: dihedral pdb=" CA SER H 20 " pdb=" C SER H 20 " pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta harmonic sigma weight residual 180.00 46.16 133.84 0 5.00e+00 4.00e-02 7.16e+02 dihedral pdb=" CA ILE H 26 " pdb=" C ILE H 26 " pdb=" N GLY H 27 " pdb=" CA GLY H 27 " ideal model delta harmonic sigma weight residual 180.00 116.21 63.79 0 5.00e+00 4.00e-02 1.63e+02 dihedral pdb=" CA ILE G 26 " pdb=" C ILE G 26 " pdb=" N GLY G 27 " pdb=" CA GLY G 27 " ideal model delta harmonic sigma weight residual 180.00 120.81 59.19 0 5.00e+00 4.00e-02 1.40e+02 ... (remaining 11983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2711 0.100 - 0.200: 299 0.200 - 0.300: 33 0.300 - 0.399: 4 0.399 - 0.499: 3 Chirality restraints: 3050 Sorted by residual: chirality pdb=" CB ILE A 708 " pdb=" CA ILE A 708 " pdb=" CG1 ILE A 708 " pdb=" CG2 ILE A 708 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.23e+00 chirality pdb=" CB VAL B 131 " pdb=" CA VAL B 131 " pdb=" CG1 VAL B 131 " pdb=" CG2 VAL B 131 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" C1' A T 29 " pdb=" O4' A T 29 " pdb=" C2' A T 29 " pdb=" N9 A T 29 " both_signs ideal model delta sigma weight residual False 2.44 2.03 0.41 2.00e-01 2.50e+01 4.19e+00 ... (remaining 3047 not shown) Planarity restraints: 3212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET H 15 " -0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C MET H 15 " 0.065 2.00e-02 2.50e+03 pdb=" O MET H 15 " -0.025 2.00e-02 2.50e+03 pdb=" N HIS H 16 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 137 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" CD GLU C 137 " 0.059 2.00e-02 2.50e+03 pdb=" OE1 GLU C 137 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU C 137 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 15 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C MET G 15 " 0.056 2.00e-02 2.50e+03 pdb=" O MET G 15 " -0.022 2.00e-02 2.50e+03 pdb=" N HIS G 16 " -0.018 2.00e-02 2.50e+03 ... (remaining 3209 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1373 2.71 - 3.26: 19283 3.26 - 3.81: 34177 3.81 - 4.35: 41684 4.35 - 4.90: 68043 Nonbonded interactions: 164560 Sorted by model distance: nonbonded pdb=" OG SER B 128 " pdb=" OH TYR B 186 " model vdw 2.166 2.440 nonbonded pdb=" OH TYR B 232 " pdb=" O TYR A 383 " model vdw 2.200 2.440 nonbonded pdb=" OG SER F 47 " pdb=" OP1 A R 9 " model vdw 2.218 2.440 nonbonded pdb=" OG SER C 55 " pdb=" OP2 U T 22 " model vdw 2.240 2.440 nonbonded pdb=" OG SER H 47 " pdb=" OP1 A R 21 " model vdw 2.243 2.440 ... (remaining 164555 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 'C' and resid 12 through 146) selection = chain 'D' } ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 1 through 65 or resid 73 through 214)) selection = (chain 'H' and (resid 1 through 65 or resid 73 through 214)) } 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=0.50 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.630 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 57.420 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.009 0.106 19742 Z= 0.572 Angle : 1.238 20.371 26888 Z= 0.678 Chirality : 0.067 0.499 3050 Planarity : 0.006 0.052 3212 Dihedral : 17.199 173.125 7793 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.04 % Favored : 89.83 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.15), residues: 2202 helix: -2.11 (0.15), residues: 827 sheet: -1.71 (0.27), residues: 323 loop : -2.70 (0.16), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 186 HIS 0.009 0.002 HIS J 282 PHE 0.049 0.004 PHE J 255 TYR 0.036 0.004 TYR J 283 ARG 0.020 0.001 ARG D 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.230 Fit side-chains revert: symmetry clash REVERT: F 120 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6603 (mm-30) REVERT: H 55 TYR cc_start: 0.8762 (t80) cc_final: 0.8487 (t80) REVERT: A 86 MET cc_start: 0.2028 (mpp) cc_final: 0.1611 (mpp) REVERT: A 250 MET cc_start: 0.8612 (tmm) cc_final: 0.8124 (tmm) REVERT: A 447 MET cc_start: 0.8166 (ptt) cc_final: 0.7550 (ptt) REVERT: A 453 MET cc_start: 0.8017 (ttm) cc_final: 0.7631 (ttm) REVERT: A 580 MET cc_start: 0.7654 (mtm) cc_final: 0.7385 (mtm) REVERT: J 292 ARG cc_start: 0.8270 (tpp80) cc_final: 0.7938 (tpp80) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3091 time to fit residues: 54.1771 Evaluate side-chains 81 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 131 optimal weight: 40.0000 chunk 204 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 HIS H 192 ASN D 75 ASN J 74 ASN J 92 GLN ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19742 Z= 0.165 Angle : 0.645 16.242 26888 Z= 0.342 Chirality : 0.042 0.200 3050 Planarity : 0.004 0.054 3212 Dihedral : 16.310 168.370 3392 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.27 % Favored : 92.55 % Rotamer: Outliers : 0.41 % Allowed : 6.92 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.61 (0.16), residues: 2202 helix: -0.86 (0.17), residues: 845 sheet: -1.51 (0.25), residues: 369 loop : -2.59 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 186 HIS 0.005 0.001 HIS H 16 PHE 0.035 0.001 PHE A 36 TYR 0.014 0.001 TYR J 283 ARG 0.006 0.000 ARG J 311 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 194 LEU cc_start: 0.8582 (tt) cc_final: 0.8317 (tt) REVERT: F 1 MET cc_start: 0.7354 (tpp) cc_final: 0.7137 (tpp) REVERT: F 120 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6498 (mm-30) REVERT: C 76 ASP cc_start: 0.8237 (p0) cc_final: 0.7762 (t70) REVERT: A 86 MET cc_start: 0.2079 (mpp) cc_final: 0.1630 (mpp) REVERT: A 249 MET cc_start: 0.5569 (tpt) cc_final: 0.5341 (tpt) REVERT: A 250 MET cc_start: 0.8565 (tmm) cc_final: 0.8088 (tmm) REVERT: A 254 MET cc_start: 0.8558 (mmm) cc_final: 0.8345 (mmm) REVERT: A 447 MET cc_start: 0.8059 (ptt) cc_final: 0.7747 (ptp) REVERT: A 453 MET cc_start: 0.8226 (ttm) cc_final: 0.7945 (ttt) REVERT: J 292 ARG cc_start: 0.8137 (tpp80) cc_final: 0.7910 (tpp80) outliers start: 8 outliers final: 3 residues processed: 109 average time/residue: 0.3049 time to fit residues: 54.0277 Evaluate side-chains 87 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 225 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 113 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 204 optimal weight: 0.0070 chunk 221 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 202 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 164 optimal weight: 0.0470 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 19742 Z= 0.148 Angle : 0.574 15.571 26888 Z= 0.304 Chirality : 0.040 0.188 3050 Planarity : 0.003 0.051 3212 Dihedral : 15.898 169.253 3392 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.90 % Favored : 91.96 % Rotamer: Outliers : 0.83 % Allowed : 10.84 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.17), residues: 2202 helix: -0.25 (0.18), residues: 853 sheet: -1.44 (0.26), residues: 367 loop : -2.43 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 186 HIS 0.003 0.001 HIS H 16 PHE 0.028 0.001 PHE A 36 TYR 0.015 0.001 TYR A 77 ARG 0.004 0.000 ARG D 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 194 LEU cc_start: 0.8617 (tt) cc_final: 0.8346 (tt) REVERT: F 6 GLU cc_start: 0.7175 (tp30) cc_final: 0.6904 (tp30) REVERT: F 120 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6485 (mm-30) REVERT: C 76 ASP cc_start: 0.8223 (p0) cc_final: 0.7824 (t70) REVERT: A 8 CYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6980 (p) REVERT: A 86 MET cc_start: 0.1935 (mpp) cc_final: 0.1517 (mpp) REVERT: A 249 MET cc_start: 0.5563 (tpt) cc_final: 0.5231 (tpt) REVERT: A 250 MET cc_start: 0.8688 (tmm) cc_final: 0.8183 (tmm) REVERT: A 447 MET cc_start: 0.7976 (ptt) cc_final: 0.7602 (ptp) REVERT: A 453 MET cc_start: 0.8345 (ttm) cc_final: 0.8045 (ttt) REVERT: J 292 ARG cc_start: 0.8068 (tpp80) cc_final: 0.7854 (tpp80) outliers start: 16 outliers final: 6 residues processed: 112 average time/residue: 0.2865 time to fit residues: 54.4070 Evaluate side-chains 98 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 225 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 202 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 137 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 chunk 217 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 194 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 124 ASN ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 HIS ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19742 Z= 0.324 Angle : 0.669 15.794 26888 Z= 0.354 Chirality : 0.044 0.260 3050 Planarity : 0.004 0.052 3212 Dihedral : 16.332 169.932 3392 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.36 % Favored : 90.51 % Rotamer: Outliers : 1.39 % Allowed : 13.32 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.17), residues: 2202 helix: 0.01 (0.18), residues: 858 sheet: -1.38 (0.26), residues: 349 loop : -2.44 (0.18), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 186 HIS 0.006 0.001 HIS H 16 PHE 0.022 0.002 PHE D 129 TYR 0.016 0.002 TYR B 186 ARG 0.004 0.001 ARG D 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 89 time to evaluate : 2.228 Fit side-chains revert: symmetry clash REVERT: B 194 LEU cc_start: 0.8663 (tt) cc_final: 0.8395 (tt) REVERT: F 120 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6654 (mm-30) REVERT: C 39 HIS cc_start: 0.7486 (m90) cc_final: 0.7030 (m90) REVERT: C 76 ASP cc_start: 0.8313 (p0) cc_final: 0.7756 (t70) REVERT: C 109 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7422 (tm-30) REVERT: D 86 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8380 (m-30) REVERT: A 8 CYS cc_start: 0.7023 (t) cc_final: 0.6681 (p) REVERT: A 86 MET cc_start: 0.1729 (mpp) cc_final: 0.1447 (mtt) REVERT: A 249 MET cc_start: 0.5648 (tpt) cc_final: 0.5447 (tpt) REVERT: A 250 MET cc_start: 0.8597 (tmm) cc_final: 0.8020 (tmm) REVERT: A 447 MET cc_start: 0.8002 (ptt) cc_final: 0.7620 (ptp) outliers start: 27 outliers final: 11 residues processed: 109 average time/residue: 0.2812 time to fit residues: 51.9177 Evaluate side-chains 92 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 210 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 82 ASN Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 254 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 181 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 124 ASN F 131 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19742 Z= 0.218 Angle : 0.603 15.413 26888 Z= 0.316 Chirality : 0.042 0.210 3050 Planarity : 0.003 0.055 3212 Dihedral : 16.037 168.190 3392 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.04 % Favored : 91.83 % Rotamer: Outliers : 1.60 % Allowed : 14.46 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.75 (0.17), residues: 2202 helix: 0.23 (0.18), residues: 850 sheet: -1.29 (0.26), residues: 349 loop : -2.38 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 186 HIS 0.004 0.001 HIS H 16 PHE 0.016 0.001 PHE A 36 TYR 0.014 0.001 TYR B 257 ARG 0.003 0.000 ARG C 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 94 time to evaluate : 2.351 Fit side-chains revert: symmetry clash REVERT: B 194 LEU cc_start: 0.8667 (tt) cc_final: 0.8406 (tt) REVERT: F 120 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6436 (mm-30) REVERT: C 39 HIS cc_start: 0.7400 (m90) cc_final: 0.6985 (m90) REVERT: C 62 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: C 76 ASP cc_start: 0.8308 (p0) cc_final: 0.7750 (t70) REVERT: C 109 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7427 (tm-30) REVERT: D 39 HIS cc_start: 0.8052 (m90) cc_final: 0.7687 (m-70) REVERT: D 86 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8375 (m-30) REVERT: A 250 MET cc_start: 0.8640 (tmm) cc_final: 0.8102 (tmm) outliers start: 31 outliers final: 18 residues processed: 117 average time/residue: 0.2649 time to fit residues: 53.3562 Evaluate side-chains 106 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 210 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 254 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 73 optimal weight: 5.9990 chunk 195 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 127 optimal weight: 30.0000 chunk 53 optimal weight: 0.8980 chunk 217 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 124 ASN H 121 ASN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 5 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19742 Z= 0.319 Angle : 0.665 15.537 26888 Z= 0.349 Chirality : 0.043 0.252 3050 Planarity : 0.004 0.057 3212 Dihedral : 16.229 166.945 3392 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.22 % Favored : 90.60 % Rotamer: Outliers : 2.12 % Allowed : 15.23 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.17), residues: 2202 helix: 0.18 (0.18), residues: 849 sheet: -1.32 (0.26), residues: 346 loop : -2.37 (0.18), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 186 HIS 0.005 0.001 HIS H 16 PHE 0.019 0.002 PHE D 129 TYR 0.016 0.002 TYR A 74 ARG 0.004 0.000 ARG F 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 91 time to evaluate : 2.350 Fit side-chains revert: symmetry clash REVERT: B 194 LEU cc_start: 0.8665 (tt) cc_final: 0.8413 (tt) REVERT: F 120 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6708 (mm-30) REVERT: G 167 GLN cc_start: 0.7624 (pt0) cc_final: 0.7315 (tm-30) REVERT: C 39 HIS cc_start: 0.7349 (m90) cc_final: 0.6988 (m90) REVERT: C 62 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: C 76 ASP cc_start: 0.8292 (p0) cc_final: 0.7762 (t70) REVERT: C 89 TYR cc_start: 0.8547 (t80) cc_final: 0.8285 (t80) REVERT: C 109 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7514 (tm-30) REVERT: D 39 HIS cc_start: 0.7917 (m90) cc_final: 0.7544 (m-70) REVERT: D 86 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8381 (m-30) REVERT: A 142 PRO cc_start: 0.4817 (Cg_exo) cc_final: 0.4556 (Cg_endo) REVERT: A 250 MET cc_start: 0.8622 (tmm) cc_final: 0.8060 (tmm) REVERT: A 447 MET cc_start: 0.7907 (ptt) cc_final: 0.7592 (ptp) outliers start: 41 outliers final: 25 residues processed: 123 average time/residue: 0.2640 time to fit residues: 56.6785 Evaluate side-chains 115 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 88 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 210 GLU Chi-restraints excluded: chain G residue 22 ASP Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain D residue 82 ASN Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 254 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 209 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 158 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 132 optimal weight: 30.0000 chunk 100 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN F 121 ASN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.112 19742 Z= 0.537 Angle : 0.840 16.609 26888 Z= 0.439 Chirality : 0.049 0.331 3050 Planarity : 0.005 0.053 3212 Dihedral : 16.850 170.018 3392 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 24.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.44 % Favored : 88.37 % Rotamer: Outliers : 2.37 % Allowed : 16.21 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.19 (0.17), residues: 2202 helix: -0.21 (0.17), residues: 848 sheet: -1.51 (0.26), residues: 342 loop : -2.55 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 186 HIS 0.007 0.002 HIS J 282 PHE 0.025 0.002 PHE F 162 TYR 0.030 0.003 TYR B 186 ARG 0.006 0.001 ARG F 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 87 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 94 LYS cc_start: 0.8242 (pttm) cc_final: 0.7628 (mtpt) REVERT: B 194 LEU cc_start: 0.8719 (tt) cc_final: 0.8499 (tt) REVERT: G 167 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: C 39 HIS cc_start: 0.7400 (m90) cc_final: 0.7169 (m-70) REVERT: C 109 GLN cc_start: 0.8443 (mm-40) cc_final: 0.7719 (tm-30) REVERT: A 142 PRO cc_start: 0.4889 (Cg_exo) cc_final: 0.4632 (Cg_endo) REVERT: A 250 MET cc_start: 0.8590 (tmm) cc_final: 0.8172 (tmm) REVERT: A 447 MET cc_start: 0.8094 (ptt) cc_final: 0.7757 (ptp) outliers start: 46 outliers final: 32 residues processed: 127 average time/residue: 0.2603 time to fit residues: 55.4350 Evaluate side-chains 116 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 83 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 210 GLU Chi-restraints excluded: chain G residue 22 ASP Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 167 GLN Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 82 ASN Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 347 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 134 optimal weight: 0.0770 chunk 86 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 137 optimal weight: 30.0000 chunk 147 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 chunk 197 optimal weight: 1.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 97 ASN A 290 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19742 Z= 0.179 Angle : 0.613 14.992 26888 Z= 0.320 Chirality : 0.042 0.195 3050 Planarity : 0.003 0.053 3212 Dihedral : 16.098 166.139 3392 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.08 % Favored : 91.78 % Rotamer: Outliers : 1.81 % Allowed : 16.93 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.80 (0.17), residues: 2202 helix: 0.26 (0.18), residues: 849 sheet: -1.51 (0.26), residues: 343 loop : -2.40 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 186 HIS 0.004 0.001 HIS B 282 PHE 0.015 0.001 PHE A 553 TYR 0.015 0.001 TYR F 55 ARG 0.003 0.000 ARG F 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 93 time to evaluate : 2.118 Fit side-chains revert: symmetry clash REVERT: B 194 LEU cc_start: 0.8676 (tt) cc_final: 0.8404 (tt) REVERT: H 53 MET cc_start: 0.8749 (ttm) cc_final: 0.8543 (ttm) REVERT: G 15 MET cc_start: 0.8406 (ttp) cc_final: 0.8205 (ttt) REVERT: G 167 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7256 (tm-30) REVERT: G 210 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8618 (tm-30) REVERT: C 39 HIS cc_start: 0.7376 (m90) cc_final: 0.7089 (m-70) REVERT: C 62 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: C 76 ASP cc_start: 0.8290 (p0) cc_final: 0.7627 (t70) REVERT: C 109 GLN cc_start: 0.8340 (mm-40) cc_final: 0.7631 (tm-30) REVERT: D 39 HIS cc_start: 0.7982 (m90) cc_final: 0.7635 (m-70) REVERT: A 75 ILE cc_start: 0.7707 (mp) cc_final: 0.7405 (mp) REVERT: A 77 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.6955 (t80) REVERT: A 142 PRO cc_start: 0.4757 (Cg_exo) cc_final: 0.4513 (Cg_endo) REVERT: A 250 MET cc_start: 0.8579 (tmm) cc_final: 0.7994 (tmm) outliers start: 35 outliers final: 24 residues processed: 121 average time/residue: 0.2859 time to fit residues: 59.3266 Evaluate side-chains 116 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 89 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 210 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 167 GLN Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 82 ASN Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 257 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 207 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 chunk 201 optimal weight: 0.4980 chunk 132 optimal weight: 9.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 19742 Z= 0.313 Angle : 0.667 15.382 26888 Z= 0.349 Chirality : 0.043 0.237 3050 Planarity : 0.004 0.050 3212 Dihedral : 16.266 168.233 3392 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.49 % Favored : 90.33 % Rotamer: Outliers : 2.01 % Allowed : 16.99 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.80 (0.17), residues: 2202 helix: 0.25 (0.18), residues: 849 sheet: -1.49 (0.26), residues: 340 loop : -2.39 (0.18), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 186 HIS 0.005 0.001 HIS J 38 PHE 0.016 0.002 PHE D 129 TYR 0.016 0.002 TYR B 186 ARG 0.004 0.000 ARG H 187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 90 time to evaluate : 2.176 Fit side-chains revert: symmetry clash REVERT: B 94 LYS cc_start: 0.8238 (pttm) cc_final: 0.7608 (mtpt) REVERT: B 194 LEU cc_start: 0.8693 (tt) cc_final: 0.8429 (tt) REVERT: G 15 MET cc_start: 0.8587 (ttp) cc_final: 0.8287 (ttt) REVERT: G 167 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7322 (tm-30) REVERT: G 210 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8596 (tm-30) REVERT: C 39 HIS cc_start: 0.7439 (m90) cc_final: 0.7169 (m-70) REVERT: C 62 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: C 109 GLN cc_start: 0.8408 (mm-40) cc_final: 0.7726 (tm-30) REVERT: A 77 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.6947 (t80) REVERT: A 142 PRO cc_start: 0.4797 (Cg_exo) cc_final: 0.4553 (Cg_endo) REVERT: A 250 MET cc_start: 0.8585 (tmm) cc_final: 0.7978 (tmm) REVERT: J 289 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8301 (p0) outliers start: 39 outliers final: 33 residues processed: 120 average time/residue: 0.2662 time to fit residues: 54.0125 Evaluate side-chains 124 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 87 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 210 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 167 GLN Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 82 ASN Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 80 PHE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 289 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 10.0000 chunk 130 optimal weight: 50.0000 chunk 101 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 224 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 178 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 137 optimal weight: 30.0000 chunk 109 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 19742 Z= 0.353 Angle : 0.702 15.717 26888 Z= 0.367 Chirality : 0.045 0.251 3050 Planarity : 0.004 0.050 3212 Dihedral : 16.410 167.811 3392 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.08 % Favored : 89.78 % Rotamer: Outliers : 2.12 % Allowed : 17.24 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.86 (0.17), residues: 2202 helix: 0.14 (0.18), residues: 850 sheet: -1.47 (0.26), residues: 338 loop : -2.38 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 334 HIS 0.006 0.001 HIS J 38 PHE 0.017 0.002 PHE D 129 TYR 0.017 0.002 TYR B 186 ARG 0.006 0.001 ARG A 740 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 85 time to evaluate : 2.384 Fit side-chains revert: symmetry clash REVERT: B 94 LYS cc_start: 0.8252 (pttm) cc_final: 0.7622 (mtpt) REVERT: B 194 LEU cc_start: 0.8725 (tt) cc_final: 0.8479 (tt) REVERT: G 15 MET cc_start: 0.8678 (ttp) cc_final: 0.8345 (ttt) REVERT: G 167 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7344 (tm-30) REVERT: C 39 HIS cc_start: 0.7475 (m90) cc_final: 0.7232 (m-70) REVERT: C 62 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: C 109 GLN cc_start: 0.8383 (mm-40) cc_final: 0.7752 (tm-30) REVERT: A 77 TYR cc_start: 0.7474 (OUTLIER) cc_final: 0.6930 (t80) REVERT: A 142 PRO cc_start: 0.4815 (Cg_exo) cc_final: 0.4570 (Cg_endo) REVERT: A 250 MET cc_start: 0.8570 (tmm) cc_final: 0.7965 (tmm) outliers start: 41 outliers final: 37 residues processed: 118 average time/residue: 0.2647 time to fit residues: 53.3084 Evaluate side-chains 125 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 85 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 210 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 167 GLN Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 82 ASN Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 80 PHE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 347 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 190 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 22 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 156 optimal weight: 0.8980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.080248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.062633 restraints weight = 96031.114| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 4.77 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19742 Z= 0.214 Angle : 0.620 15.114 26888 Z= 0.323 Chirality : 0.042 0.193 3050 Planarity : 0.003 0.051 3212 Dihedral : 16.046 166.649 3392 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.45 % Favored : 91.42 % Rotamer: Outliers : 1.86 % Allowed : 17.50 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.73 (0.17), residues: 2202 helix: 0.30 (0.18), residues: 857 sheet: -1.45 (0.26), residues: 338 loop : -2.35 (0.18), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 186 HIS 0.003 0.001 HIS J 155 PHE 0.015 0.001 PHE A 553 TYR 0.015 0.001 TYR C 89 ARG 0.003 0.000 ARG H 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3174.71 seconds wall clock time: 60 minutes 20.34 seconds (3620.34 seconds total)