Starting phenix.real_space_refine on Sat Feb 17 07:15:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl2_25189/02_2024/7sl2_25189_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl2_25189/02_2024/7sl2_25189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl2_25189/02_2024/7sl2_25189.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl2_25189/02_2024/7sl2_25189.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl2_25189/02_2024/7sl2_25189_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl2_25189/02_2024/7sl2_25189_neut.pdb" } resolution = 3.6 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3406 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 122 5.16 5 C 9187 2.51 5 N 2489 2.21 5 O 2679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "G TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 17": "OE1" <-> "OE2" 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: 14477 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6518 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 762} Chain breaks: 8 Chain: "B" Number of atoms: 6448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 798, 6448 Classifications: {'peptide': 798} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 752} Chain breaks: 6 Chain: "C" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 214 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "D" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 199 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "E" Number of atoms: 211 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 27, 209 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 25} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 27, 209 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 25} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 213 Chain: "F" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 27} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 165 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "H" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 165 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "I" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 166 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "J" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 166 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Time building chain proxies: 7.28, per 1000 atoms: 0.50 Number of scatterers: 14477 At special positions: 0 Unit cell: (135, 141.48, 178.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 122 16.00 O 2679 8.00 N 2489 7.00 C 9187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 862 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 797 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.02 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 862 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 797 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS G 7 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS G 20 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS H 7 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS H 20 " distance=2.02 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS I 7 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS I 20 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS J 7 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS J 20 " distance=2.03 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 11 " distance=2.03 Simple disulfide: pdb=" SG CYS H 6 " - pdb=" SG CYS H 11 " distance=2.03 Simple disulfide: pdb=" SG CYS I 6 " - pdb=" SG CYS I 11 " distance=2.03 Simple disulfide: pdb=" SG CYS J 6 " - pdb=" SG CYS J 11 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.42 Conformation dependent library (CDL) restraints added in 2.8 seconds 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3382 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 33 sheets defined 17.2% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.542A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.897A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A 268 " --> pdb=" O PHE A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.725A pdb=" N GLU A 329 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.887A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 444 " --> pdb=" O HIS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 694 through 716 removed outlier: 3.541A pdb=" N PHE A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'B' and resid 16 through 24 removed outlier: 4.273A pdb=" N ARG B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 132 through 136 removed outlier: 3.520A pdb=" N ARG B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 255 through 268 removed outlier: 3.545A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 267 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN B 268 " --> pdb=" O PHE B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 318 Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 350 through 358 removed outlier: 3.661A pdb=" N ALA B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.879A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.563A pdb=" N ARG B 451 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 448 through 452' Processing helix chain 'B' and resid 640 through 644 Processing helix chain 'B' and resid 707 through 716 Processing helix chain 'B' and resid 865 through 871 Processing helix chain 'C' and resid 8 through 19 Processing helix chain 'D' and resid 8 through 18 removed outlier: 3.521A pdb=" N VAL D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 20 removed outlier: 3.773A pdb=" N VAL E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 20 Processing helix chain 'F' and resid 21 through 23 No H-bonds generated for 'chain 'F' and resid 21 through 23' Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 12 through 17 removed outlier: 3.617A pdb=" N LEU G 16 " --> pdb=" O SER G 12 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 12 through 17' Processing helix chain 'G' and resid 18 through 20 No H-bonds generated for 'chain 'G' and resid 18 through 20' Processing helix chain 'H' and resid 2 through 7 Processing helix chain 'H' and resid 12 through 19 removed outlier: 3.589A pdb=" N LEU H 16 " --> pdb=" O SER H 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 8 Processing helix chain 'I' and resid 12 through 19 removed outlier: 3.571A pdb=" N TYR I 19 " --> pdb=" O GLN I 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 7 Processing helix chain 'J' and resid 12 through 17 Processing helix chain 'J' and resid 18 through 20 No H-bonds generated for 'chain 'J' and resid 18 through 20' Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 6.425A pdb=" N HIS A 32 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 82 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 13 removed outlier: 6.425A pdb=" N HIS A 32 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU A 61 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLN A 34 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU A 63 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU A 36 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG A 65 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 216 removed outlier: 3.836A pdb=" N ALA A 227 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ASN A 215 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N CYS A 225 " --> pdb=" O ASN A 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA6, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.570A pdb=" N ILE A 364 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 320 through 321 removed outlier: 5.087A pdb=" N TYR A 398 " --> pdb=" O LYS A 425 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N PHE A 427 " --> pdb=" O TYR A 398 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE A 400 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N HIS A 429 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA A 402 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 475 through 480 removed outlier: 6.581A pdb=" N ARG A 488 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE A 478 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU A 486 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.547A pdb=" N GLY A 502 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 601 through 606 removed outlier: 6.463A pdb=" N LYS A 616 " --> pdb=" O PRO A 603 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER A 605 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 614 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 761 through 764 Processing sheet with id=AB4, first strand: chain 'A' and resid 821 through 824 Processing sheet with id=AB5, first strand: chain 'A' and resid 861 through 864 removed outlier: 3.835A pdb=" N LEU A 846 " --> pdb=" O THR A 891 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL A 888 " --> pdb=" O TRP A 899 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TRP A 899 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ALA A 890 " --> pdb=" O GLY A 897 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 882 through 883 Processing sheet with id=AB7, first strand: chain 'B' and resid 12 through 14 removed outlier: 6.618A pdb=" N LEU B 33 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N PHE B 64 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE B 35 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N VAL B 66 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU B 37 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL B 117 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL B 146 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE B 119 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASN B 148 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LYS B 121 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AB9, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AC1, first strand: chain 'B' and resid 212 through 216 removed outlier: 5.739A pdb=" N LEU B 213 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N CYS B 228 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASN B 215 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 231 through 233 Processing sheet with id=AC3, first strand: chain 'B' and resid 246 through 248 Processing sheet with id=AC4, first strand: chain 'B' and resid 292 through 294 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.684A pdb=" N ASN B 337 " --> pdb=" O CYS B 312 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N ILE B 336 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 10.972A pdb=" N GLU B 363 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 10.280A pdb=" N GLU B 391 " --> pdb=" O GLU B 363 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N SER B 365 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 319 through 321 removed outlier: 6.695A pdb=" N LEU B 368 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N LEU B 403 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE B 370 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N HIS B 429 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA B 402 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AC8, first strand: chain 'B' and resid 475 through 480 Processing sheet with id=AC9, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.753A pdb=" N GLY B 502 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 601 through 607 removed outlier: 6.998A pdb=" N LYS B 616 " --> pdb=" O PRO B 603 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N SER B 605 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE B 614 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 761 through 764 removed outlier: 3.944A pdb=" N GLU B 762 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL B 632 " --> pdb=" O GLU B 762 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN B 790 " --> pdb=" O ARG B 796 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 761 through 764 removed outlier: 3.944A pdb=" N GLU B 762 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL B 632 " --> pdb=" O GLU B 762 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 821 through 824 removed outlier: 3.646A pdb=" N CYS B 874 " --> pdb=" O LEU B 832 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 858 through 864 Processing sheet with id=AD6, first strand: chain 'E' and resid 24 through 26 345 hydrogen bonds defined for protein. 858 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.12 Time building geometry restraints manager: 6.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4743 1.34 - 1.46: 3555 1.46 - 1.58: 6381 1.58 - 1.70: 0 1.70 - 1.82: 146 Bond restraints: 14825 Sorted by residual: bond pdb=" CA GLU A 469 " pdb=" C GLU A 469 " ideal model delta sigma weight residual 1.522 1.501 0.020 1.40e-02 5.10e+03 2.12e+00 bond pdb=" CA CYS A 304 " pdb=" C CYS A 304 " ideal model delta sigma weight residual 1.524 1.505 0.019 1.32e-02 5.74e+03 2.03e+00 bond pdb=" CA LEU A 305 " pdb=" C LEU A 305 " ideal model delta sigma weight residual 1.523 1.505 0.018 1.34e-02 5.57e+03 1.76e+00 bond pdb=" C CYS B 333 " pdb=" N THR B 334 " ideal model delta sigma weight residual 1.332 1.316 0.017 1.40e-02 5.10e+03 1.40e+00 bond pdb=" CA CYS A 308 " pdb=" C CYS A 308 " ideal model delta sigma weight residual 1.517 1.528 -0.011 1.02e-02 9.61e+03 1.25e+00 ... (remaining 14820 not shown) Histogram of bond angle deviations from ideal: 99.11 - 106.10: 364 106.10 - 113.09: 7876 113.09 - 120.07: 5121 120.07 - 127.06: 6528 127.06 - 134.05: 198 Bond angle restraints: 20087 Sorted by residual: angle pdb=" N GLU A 469 " pdb=" CA GLU A 469 " pdb=" C GLU A 469 " ideal model delta sigma weight residual 112.90 104.70 8.20 1.31e+00 5.83e-01 3.92e+01 angle pdb=" N CYS A 304 " pdb=" CA CYS A 304 " pdb=" C CYS A 304 " ideal model delta sigma weight residual 111.11 105.99 5.12 1.20e+00 6.94e-01 1.82e+01 angle pdb=" C THR A 302 " pdb=" N PRO A 303 " pdb=" CA PRO A 303 " ideal model delta sigma weight residual 119.84 115.53 4.31 1.25e+00 6.40e-01 1.19e+01 angle pdb=" N GLU A 471 " pdb=" CA GLU A 471 " pdb=" C GLU A 471 " ideal model delta sigma weight residual 110.80 103.96 6.84 2.13e+00 2.20e-01 1.03e+01 angle pdb=" C LYS A 310 " pdb=" N VAL A 311 " pdb=" CA VAL A 311 " ideal model delta sigma weight residual 122.37 118.47 3.90 1.29e+00 6.01e-01 9.16e+00 ... (remaining 20082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8081 17.98 - 35.96: 737 35.96 - 53.94: 124 53.94 - 71.91: 24 71.91 - 89.89: 17 Dihedral angle restraints: 8983 sinusoidal: 3745 harmonic: 5238 Sorted by residual: dihedral pdb=" CB CYS E 19 " pdb=" SG CYS E 19 " pdb=" SG CYS I 20 " pdb=" CB CYS I 20 " ideal model delta sinusoidal sigma weight residual 93.00 175.95 -82.95 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 172.74 -79.74 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" CB CYS C 7 " pdb=" SG CYS C 7 " pdb=" SG CYS G 7 " pdb=" CB CYS G 7 " ideal model delta sinusoidal sigma weight residual 93.00 15.21 77.79 1 1.00e+01 1.00e-02 7.57e+01 ... (remaining 8980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1508 0.039 - 0.077: 455 0.077 - 0.116: 177 0.116 - 0.155: 35 0.155 - 0.194: 2 Chirality restraints: 2177 Sorted by residual: chirality pdb=" CB ILE A 342 " pdb=" CA ILE A 342 " pdb=" CG1 ILE A 342 " pdb=" CG2 ILE A 342 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.37e-01 chirality pdb=" CB ILE B 174 " pdb=" CA ILE B 174 " pdb=" CG1 ILE B 174 " pdb=" CG2 ILE B 174 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CB ILE A 370 " pdb=" CA ILE A 370 " pdb=" CG1 ILE A 370 " pdb=" CG2 ILE A 370 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 2174 not shown) Planarity restraints: 2597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 308 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO B 309 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 309 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 309 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 488 " 0.142 9.50e-02 1.11e+02 6.39e-02 2.70e+00 pdb=" NE ARG B 488 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 488 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 488 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 488 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 655 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 656 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 656 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 656 " -0.017 5.00e-02 4.00e+02 ... (remaining 2594 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 399 2.70 - 3.25: 14171 3.25 - 3.80: 22931 3.80 - 4.35: 29755 4.35 - 4.90: 48791 Nonbonded interactions: 116047 Sorted by model distance: nonbonded pdb=" OG1 THR A 130 " pdb=" O CYS A 182 " model vdw 2.147 2.440 nonbonded pdb=" OD1 ASN B 175 " pdb=" N GLY B 176 " model vdw 2.167 2.520 nonbonded pdb=" OG1 THR B 41 " pdb=" O TYR B 67 " model vdw 2.195 2.440 nonbonded pdb=" O GLN G 5 " pdb=" OG SER G 9 " model vdw 2.212 2.440 nonbonded pdb=" O LEU B 643 " pdb=" OH TYR B 648 " model vdw 2.221 2.440 ... (remaining 116042 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 3 through 518 or resid 528 through 658 or resid 706 throug \ h 907)) selection = (chain 'B' and (resid 3 through 314 or resid 317 through 346 or resid 351 throug \ h 539 or resid 549 through 719 or resid 758 through 907)) } ncs_group { reference = (chain 'C' and (resid 4 through 8 or resid 10 through 20 or (resid 21 and (name \ N or name CA or name C or name O or name CB or name CG )) or resid 22 through 28 \ )) selection = (chain 'D' and (resid 4 through 8 or resid 10 through 20 or (resid 21 and (name \ N or name CA or name C or name O or name CB or name CG )) or resid 22 through 28 \ )) selection = (chain 'E' and (resid 4 through 8 or resid 10 through 28)) selection = (chain 'F' and (resid 4 through 8 or resid 10 through 20 or (resid 21 and (name \ N or name CA or name C or name O or name CB or name CG )) or resid 22 through 28 \ )) } ncs_group { reference = chain 'G' selection = chain 'H' selection = (chain 'I' and (resid 1 through 20 or (resid 21 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2)))) selection = (chain 'J' and (resid 1 through 20 or (resid 21 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2)))) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 6.480 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 39.870 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.100 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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 : 0.003 0.035 14825 Z= 0.210 Angle : 0.563 8.197 20087 Z= 0.297 Chirality : 0.044 0.194 2177 Planarity : 0.003 0.064 2597 Dihedral : 13.631 89.893 5466 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.04 % Favored : 92.73 % Rotamer: Outliers : 0.18 % Allowed : 0.25 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.21), residues: 1748 helix: -0.29 (0.36), residues: 217 sheet: 0.55 (0.30), residues: 358 loop : -0.99 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 834 HIS 0.005 0.001 HIS A 199 PHE 0.020 0.001 PHE B 778 TYR 0.016 0.001 TYR G 14 ARG 0.008 0.000 ARG B 488 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 1.737 Fit side-chains revert: symmetry clash REVERT: B 294 MET cc_start: 0.7996 (tmm) cc_final: 0.7766 (tmm) REVERT: J 4 GLU cc_start: 0.8338 (mp0) cc_final: 0.7766 (mp0) outliers start: 3 outliers final: 1 residues processed: 69 average time/residue: 0.2149 time to fit residues: 25.8243 Evaluate side-chains 46 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 chunk 137 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 158 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 4 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.0725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14825 Z= 0.262 Angle : 0.545 6.836 20087 Z= 0.283 Chirality : 0.044 0.199 2177 Planarity : 0.004 0.038 2597 Dihedral : 4.406 38.003 1963 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.74 % Allowed : 5.40 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.21), residues: 1748 helix: -0.27 (0.36), residues: 223 sheet: 0.32 (0.29), residues: 364 loop : -0.94 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 414 HIS 0.015 0.001 HIS B 867 PHE 0.021 0.001 PHE A 518 TYR 0.016 0.001 TYR B 401 ARG 0.006 0.000 ARG B 488 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 1.749 Fit side-chains revert: symmetry clash REVERT: J 4 GLU cc_start: 0.8444 (mp0) cc_final: 0.7852 (mp0) REVERT: J 21 ASN cc_start: 0.7262 (m110) cc_final: 0.6864 (m-40) outliers start: 12 outliers final: 8 residues processed: 57 average time/residue: 0.2067 time to fit residues: 20.9630 Evaluate side-chains 55 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain G residue 14 TYR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain J residue 8 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 159 optimal weight: 0.0980 chunk 171 optimal weight: 3.9990 chunk 141 optimal weight: 20.0000 chunk 157 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14825 Z= 0.160 Angle : 0.496 7.802 20087 Z= 0.256 Chirality : 0.043 0.180 2177 Planarity : 0.003 0.031 2597 Dihedral : 4.295 40.433 1963 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.80 % Allowed : 8.16 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.21), residues: 1748 helix: -0.30 (0.35), residues: 229 sheet: 0.32 (0.29), residues: 368 loop : -0.94 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 414 HIS 0.003 0.001 HIS A 199 PHE 0.016 0.001 PHE A 518 TYR 0.008 0.001 TYR A 292 ARG 0.003 0.000 ARG B 488 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 1.801 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7035 (mtp) REVERT: J 4 GLU cc_start: 0.8481 (mp0) cc_final: 0.7902 (mp0) outliers start: 13 outliers final: 9 residues processed: 55 average time/residue: 0.2217 time to fit residues: 21.6114 Evaluate side-chains 56 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain G residue 14 TYR Chi-restraints excluded: chain I residue 3 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 159 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN B 185 HIS B 295 ASN B 407 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14825 Z= 0.277 Angle : 0.536 6.845 20087 Z= 0.277 Chirality : 0.044 0.178 2177 Planarity : 0.003 0.033 2597 Dihedral : 4.460 39.810 1963 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 1.10 % Allowed : 10.80 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.21), residues: 1748 helix: -0.14 (0.36), residues: 220 sheet: 0.15 (0.29), residues: 363 loop : -0.96 (0.19), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 414 HIS 0.007 0.001 HIS A 199 PHE 0.018 0.001 PHE A 518 TYR 0.016 0.001 TYR B 401 ARG 0.003 0.000 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 48 time to evaluate : 1.702 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7151 (mtp) REVERT: B 294 MET cc_start: 0.8014 (tmm) cc_final: 0.7758 (tmm) REVERT: J 4 GLU cc_start: 0.8502 (mp0) cc_final: 0.7907 (mp0) REVERT: J 21 ASN cc_start: 0.7462 (m110) cc_final: 0.6895 (m110) outliers start: 18 outliers final: 11 residues processed: 60 average time/residue: 0.2502 time to fit residues: 25.0263 Evaluate side-chains 58 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain G residue 14 TYR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain J residue 8 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 6.9990 chunk 96 optimal weight: 0.0000 chunk 2 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 151 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 591 GLN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14825 Z= 0.137 Angle : 0.486 8.541 20087 Z= 0.251 Chirality : 0.043 0.167 2177 Planarity : 0.003 0.031 2597 Dihedral : 4.181 23.733 1962 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.98 % Allowed : 12.15 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.21), residues: 1748 helix: -0.28 (0.35), residues: 230 sheet: 0.25 (0.29), residues: 363 loop : -0.94 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 414 HIS 0.003 0.000 HIS A 199 PHE 0.015 0.001 PHE A 518 TYR 0.008 0.001 TYR A 581 ARG 0.005 0.000 ARG J 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 51 time to evaluate : 1.840 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7233 (mtp) REVERT: B 645 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: J 4 GLU cc_start: 0.8525 (mp0) cc_final: 0.7928 (mp0) REVERT: J 21 ASN cc_start: 0.7337 (m110) cc_final: 0.6821 (m110) outliers start: 16 outliers final: 6 residues processed: 62 average time/residue: 0.2224 time to fit residues: 23.6151 Evaluate side-chains 54 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain I residue 3 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 7.9990 chunk 152 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 169 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14825 Z= 0.256 Angle : 0.530 8.120 20087 Z= 0.271 Chirality : 0.043 0.166 2177 Planarity : 0.003 0.032 2597 Dihedral : 4.297 25.127 1962 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.92 % Allowed : 13.08 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.21), residues: 1748 helix: -0.31 (0.36), residues: 229 sheet: 0.11 (0.29), residues: 363 loop : -0.96 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 414 HIS 0.004 0.001 HIS B 712 PHE 0.016 0.001 PHE A 518 TYR 0.012 0.001 TYR B 401 ARG 0.003 0.000 ARG J 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 48 time to evaluate : 1.531 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7084 (mtp) REVERT: B 645 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: J 4 GLU cc_start: 0.8532 (mp0) cc_final: 0.7915 (mp0) REVERT: J 21 ASN cc_start: 0.7451 (m110) cc_final: 0.6864 (m110) outliers start: 15 outliers final: 10 residues processed: 58 average time/residue: 0.2115 time to fit residues: 21.2431 Evaluate side-chains 59 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain I residue 3 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 8.9990 chunk 96 optimal weight: 0.0770 chunk 123 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14825 Z= 0.145 Angle : 0.490 8.133 20087 Z= 0.250 Chirality : 0.042 0.161 2177 Planarity : 0.003 0.032 2597 Dihedral : 4.155 23.490 1962 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.86 % Allowed : 13.63 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.21), residues: 1748 helix: -0.30 (0.35), residues: 229 sheet: 0.26 (0.29), residues: 358 loop : -0.92 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 414 HIS 0.002 0.000 HIS B 712 PHE 0.014 0.001 PHE A 518 TYR 0.008 0.001 TYR A 581 ARG 0.002 0.000 ARG J 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 1.676 Fit side-chains revert: symmetry clash REVERT: B 645 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: J 4 GLU cc_start: 0.8547 (mp0) cc_final: 0.7968 (mp0) REVERT: J 21 ASN cc_start: 0.7351 (m110) cc_final: 0.6734 (m110) outliers start: 14 outliers final: 9 residues processed: 62 average time/residue: 0.2034 time to fit residues: 22.4468 Evaluate side-chains 57 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain J residue 8 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14825 Z= 0.225 Angle : 0.519 7.824 20087 Z= 0.265 Chirality : 0.043 0.160 2177 Planarity : 0.003 0.032 2597 Dihedral : 4.234 23.921 1962 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.23 % Allowed : 13.81 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.21), residues: 1748 helix: -0.29 (0.36), residues: 229 sheet: 0.15 (0.29), residues: 363 loop : -0.93 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 414 HIS 0.003 0.001 HIS A 199 PHE 0.015 0.001 PHE A 518 TYR 0.011 0.001 TYR A 292 ARG 0.003 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 47 time to evaluate : 1.691 Fit side-chains revert: symmetry clash REVERT: B 645 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: J 4 GLU cc_start: 0.8540 (mp0) cc_final: 0.7919 (mp0) REVERT: J 21 ASN cc_start: 0.7368 (m110) cc_final: 0.6820 (m110) outliers start: 20 outliers final: 16 residues processed: 62 average time/residue: 0.2065 time to fit residues: 22.9187 Evaluate side-chains 64 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 47 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 14 TYR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain J residue 8 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14825 Z= 0.183 Angle : 0.507 8.400 20087 Z= 0.258 Chirality : 0.043 0.161 2177 Planarity : 0.003 0.032 2597 Dihedral : 4.215 24.160 1962 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.23 % Allowed : 14.12 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.21), residues: 1748 helix: -0.32 (0.35), residues: 229 sheet: 0.13 (0.29), residues: 363 loop : -0.92 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 414 HIS 0.002 0.001 HIS B 712 PHE 0.015 0.001 PHE A 518 TYR 0.010 0.001 TYR A 507 ARG 0.002 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 49 time to evaluate : 1.761 Fit side-chains revert: symmetry clash REVERT: B 645 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: J 4 GLU cc_start: 0.8541 (mp0) cc_final: 0.7926 (mp0) REVERT: J 21 ASN cc_start: 0.7333 (m110) cc_final: 0.6737 (m110) outliers start: 20 outliers final: 16 residues processed: 63 average time/residue: 0.2118 time to fit residues: 23.6127 Evaluate side-chains 65 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 48 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain J residue 8 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 138 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14825 Z= 0.229 Angle : 0.534 8.571 20087 Z= 0.270 Chirality : 0.043 0.160 2177 Planarity : 0.003 0.032 2597 Dihedral : 4.291 24.719 1962 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.10 % Allowed : 14.18 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.21), residues: 1748 helix: -0.33 (0.36), residues: 229 sheet: 0.09 (0.29), residues: 363 loop : -0.93 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 414 HIS 0.003 0.001 HIS A 199 PHE 0.015 0.001 PHE A 518 TYR 0.012 0.001 TYR B 507 ARG 0.003 0.000 ARG B 556 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 49 time to evaluate : 1.701 Fit side-chains revert: symmetry clash REVERT: B 645 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: J 4 GLU cc_start: 0.8543 (mp0) cc_final: 0.7918 (mp0) REVERT: J 21 ASN cc_start: 0.7370 (m110) cc_final: 0.6760 (m110) outliers start: 18 outliers final: 15 residues processed: 62 average time/residue: 0.2114 time to fit residues: 23.2727 Evaluate side-chains 65 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 49 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain J residue 8 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.069351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.050140 restraints weight = 73200.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.051578 restraints weight = 36593.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.052427 restraints weight = 24408.644| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14825 Z= 0.255 Angle : 0.544 11.239 20087 Z= 0.276 Chirality : 0.043 0.160 2177 Planarity : 0.003 0.032 2597 Dihedral : 4.429 28.022 1962 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 1.29 % Allowed : 14.18 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.21), residues: 1748 helix: -0.19 (0.36), residues: 219 sheet: 0.02 (0.29), residues: 363 loop : -0.95 (0.19), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 834 HIS 0.004 0.001 HIS A 199 PHE 0.016 0.001 PHE A 518 TYR 0.018 0.001 TYR B 507 ARG 0.003 0.000 ARG F 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2392.75 seconds wall clock time: 45 minutes 8.27 seconds (2708.27 seconds total)