Starting phenix.real_space_refine on Sun Apr 7 20:14:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mjz_9135/04_2024/6mjz_9135.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mjz_9135/04_2024/6mjz_9135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mjz_9135/04_2024/6mjz_9135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mjz_9135/04_2024/6mjz_9135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mjz_9135/04_2024/6mjz_9135.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mjz_9135/04_2024/6mjz_9135.pdb" } resolution = 4.3 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= 0.007 sd= 0.110 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 7228 2.51 5 N 1914 2.21 5 O 2235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 47": "NH1" <-> "NH2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A ARG 77": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "B ARG 47": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 47": "NH1" <-> "NH2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ARG 152": "NH1" <-> "NH2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C ARG 236": "NH1" <-> "NH2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "C ARG 281": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 400": "NH1" <-> "NH2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 26": "NH1" <-> "NH2" Residue "L PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11436 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3291 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3162 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3218 Classifications: {'peptide': 415} Link IDs: {'CIS': 2, 'PTRANS': 15, 'TRANS': 397} Chain breaks: 1 Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 928 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "L" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 99} Time building chain proxies: 6.24, per 1000 atoms: 0.55 Number of scatterers: 11436 At special positions: 0 Unit cell: (101.2, 101.2, 158.4, 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 59 16.00 O 2235 8.00 N 1914 7.00 C 7228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 192 " distance=2.53 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 168 " distance=2.52 Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 230 " distance=2.18 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.36 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.25 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.29 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.53 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 192 " distance=2.35 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 168 " distance=2.34 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 230 " distance=2.27 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.52 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.15 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.33 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.25 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 192 " distance=2.84 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 168 " distance=2.30 Simple disulfide: pdb=" SG CYS C 213 " - pdb=" SG CYS C 230 " distance=2.57 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.43 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.10 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.40 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.29 Simple disulfide: pdb=" SG CYS L 25 " - pdb=" SG CYS L 90 " distance=2.56 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: 4.53 Conformation dependent library (CDL) restraints added in 2.2 seconds 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2778 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 23 sheets defined 31.4% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 removed outlier: 3.546A pdb=" N HIS A 27 " --> pdb=" O LYS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 89 removed outlier: 3.516A pdb=" N ASP A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 124 through 139 removed outlier: 3.508A pdb=" N ILE A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 148 through 154 removed outlier: 4.297A pdb=" N ARG A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 187 removed outlier: 4.699A pdb=" N LYS A 181 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL A 184 " --> pdb=" O ASN A 180 " (cutoff:3.500A) Proline residue: A 185 - end of helix Processing helix chain 'A' and resid 191 through 212 removed outlier: 4.041A pdb=" N ALA A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 235 removed outlier: 4.218A pdb=" N TYR A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 removed outlier: 4.303A pdb=" N THR A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 358 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 452 through 471 removed outlier: 3.513A pdb=" N ILE A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 69 through 80 removed outlier: 3.951A pdb=" N ARG B 73 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 74 " --> pdb=" O GLN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 90 removed outlier: 4.018A pdb=" N LYS B 87 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU B 88 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN B 89 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 153 removed outlier: 4.551A pdb=" N SER B 142 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ASP B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 187 removed outlier: 4.489A pdb=" N VAL B 184 " --> pdb=" O ASN B 180 " (cutoff:3.500A) Proline residue: B 185 - end of helix Processing helix chain 'B' and resid 191 through 214 removed outlier: 4.118A pdb=" N ALA B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N CYS B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 235 removed outlier: 3.894A pdb=" N ILE B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR B 235 " --> pdb=" O ILE B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 246 removed outlier: 4.510A pdb=" N GLU B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 removed outlier: 3.796A pdb=" N THR B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 358 removed outlier: 4.160A pdb=" N CYS B 355 " --> pdb=" O GLU B 351 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.601A pdb=" N GLN B 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 452 through 471 removed outlier: 3.854A pdb=" N ILE B 456 " --> pdb=" O ASP B 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 29 removed outlier: 4.356A pdb=" N HIS C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 77 removed outlier: 3.889A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN C 70 " --> pdb=" O GLN C 66 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR C 71 " --> pdb=" O GLN C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 137 removed outlier: 4.409A pdb=" N LEU C 134 " --> pdb=" O ALA C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 152 removed outlier: 4.043A pdb=" N LYS C 146 " --> pdb=" O SER C 142 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU C 147 " --> pdb=" O ASP C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 187 removed outlier: 4.769A pdb=" N VAL C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) Proline residue: C 185 - end of helix Processing helix chain 'C' and resid 191 through 214 removed outlier: 4.140A pdb=" N CYS C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 235 Processing helix chain 'C' and resid 235 through 240 Processing helix chain 'C' and resid 242 through 247 removed outlier: 4.081A pdb=" N THR C 247 " --> pdb=" O PHE C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 358 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 452 through 473 Processing helix chain 'H' and resid 61 through 64 Processing sheet with id=AA1, first strand: chain 'A' and resid 285 through 287 removed outlier: 4.507A pdb=" N THR A 286 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE A 40 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 159 removed outlier: 3.678A pdb=" N VAL A 170 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 172 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 52 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP A 268 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 226 through 227 removed outlier: 3.975A pdb=" N ILE A 226 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 295 removed outlier: 3.615A pdb=" N GLY A 324 " --> pdb=" O MET A 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302 removed outlier: 4.030A pdb=" N TRP A 308 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 379 Processing sheet with id=AA7, first strand: chain 'B' and resid 31 through 32 removed outlier: 3.533A pdb=" N ASP B 297 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 10.248A pdb=" N LEU B 289 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N ILE B 40 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR B 291 " --> pdb=" O MET B 38 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET B 38 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 31 through 32 removed outlier: 3.533A pdb=" N ASP B 297 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 172 through 173 removed outlier: 4.165A pdb=" N ASP B 268 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLN B 279 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL B 266 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AB2, first strand: chain 'B' and resid 376 through 379 removed outlier: 4.555A pdb=" N ALA B 385 " --> pdb=" O LYS B 410 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS B 410 " --> pdb=" O ALA B 385 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 31 through 32 removed outlier: 3.589A pdb=" N ASP C 297 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 286 through 287 removed outlier: 3.596A pdb=" N THR C 286 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE C 40 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY C 37 " --> pdb=" O TYR C 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 46 through 48 removed outlier: 3.506A pdb=" N ASP C 268 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLN C 279 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL C 266 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 300 through 303 Processing sheet with id=AB7, first strand: chain 'C' and resid 317 through 319 Processing sheet with id=AB8, first strand: chain 'C' and resid 383 through 385 removed outlier: 3.522A pdb=" N VAL C 383 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 412 " --> pdb=" O VAL C 383 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA C 385 " --> pdb=" O LYS C 410 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS C 410 " --> pdb=" O ALA C 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'H' and resid 4 through 7 removed outlier: 4.230A pdb=" N SER H 84 " --> pdb=" O GLU H 16 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU H 16 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.824A pdb=" N LYS H 58 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER H 35 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE H 37 " --> pdb=" O PHE H 94 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 12 through 14 removed outlier: 5.799A pdb=" N LEU L 13 " --> pdb=" O GLU L 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'L' and resid 24 through 26 removed outlier: 3.590A pdb=" N THR L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 55 through 56 removed outlier: 3.655A pdb=" N THR L 55 " --> pdb=" O TYR L 51 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR L 51 " --> pdb=" O THR L 55 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N SER L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN L 39 " --> pdb=" O SER L 48 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP L 37 " --> pdb=" O ILE L 50 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 948 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: 3.30 Time building geometry restraints manager: 4.94 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: 3727 1.34 - 1.47: 2671 1.47 - 1.60: 5148 1.60 - 1.73: 0 1.73 - 1.86: 72 Bond restraints: 11618 Sorted by residual: bond pdb=" CG1 ILE B 128 " pdb=" CD1 ILE B 128 " ideal model delta sigma weight residual 1.513 1.419 0.094 3.90e-02 6.57e+02 5.86e+00 bond pdb=" CG ARG B 365 " pdb=" CD ARG B 365 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.21e+00 bond pdb=" N ILE L 98 " pdb=" CA ILE L 98 " ideal model delta sigma weight residual 1.474 1.448 0.027 1.57e-02 4.06e+03 2.91e+00 bond pdb=" CB CYS C 192 " pdb=" SG CYS C 192 " ideal model delta sigma weight residual 1.808 1.863 -0.055 3.30e-02 9.18e+02 2.77e+00 bond pdb=" CB PRO A 185 " pdb=" CG PRO A 185 " ideal model delta sigma weight residual 1.492 1.410 0.082 5.00e-02 4.00e+02 2.72e+00 ... (remaining 11613 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.31: 279 106.31 - 113.25: 6428 113.25 - 120.19: 4047 120.19 - 127.13: 4904 127.13 - 134.07: 111 Bond angle restraints: 15769 Sorted by residual: angle pdb=" C LYS C 138 " pdb=" N GLN C 139 " pdb=" CA GLN C 139 " ideal model delta sigma weight residual 120.44 129.89 -9.45 1.30e+00 5.92e-01 5.28e+01 angle pdb=" CA TYR C 71 " pdb=" CB TYR C 71 " pdb=" CG TYR C 71 " ideal model delta sigma weight residual 113.90 122.74 -8.84 1.80e+00 3.09e-01 2.41e+01 angle pdb=" N ASN C 217 " pdb=" CA ASN C 217 " pdb=" C ASN C 217 " ideal model delta sigma weight residual 110.97 116.01 -5.04 1.09e+00 8.42e-01 2.14e+01 angle pdb=" N ASN C 217 " pdb=" CA ASN C 217 " pdb=" CB ASN C 217 " ideal model delta sigma weight residual 109.91 116.60 -6.69 1.46e+00 4.69e-01 2.10e+01 angle pdb=" C GLY C 225 " pdb=" N ILE C 226 " pdb=" CA ILE C 226 " ideal model delta sigma weight residual 121.97 129.57 -7.60 1.80e+00 3.09e-01 1.78e+01 ... (remaining 15764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 6590 16.16 - 32.33: 437 32.33 - 48.49: 90 48.49 - 64.66: 18 64.66 - 80.82: 14 Dihedral angle restraints: 7149 sinusoidal: 2845 harmonic: 4304 Sorted by residual: dihedral pdb=" CA ALA C 171 " pdb=" C ALA C 171 " pdb=" N ILE C 172 " pdb=" CA ILE C 172 " ideal model delta harmonic sigma weight residual 180.00 134.92 45.08 0 5.00e+00 4.00e-02 8.13e+01 dihedral pdb=" CA ASN C 217 " pdb=" C ASN C 217 " pdb=" N ILE C 218 " pdb=" CA ILE C 218 " ideal model delta harmonic sigma weight residual 180.00 -135.07 -44.93 0 5.00e+00 4.00e-02 8.07e+01 dihedral pdb=" CA SER C 164 " pdb=" C SER C 164 " pdb=" N VAL C 165 " pdb=" CA VAL C 165 " ideal model delta harmonic sigma weight residual 180.00 -135.25 -44.75 0 5.00e+00 4.00e-02 8.01e+01 ... (remaining 7146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1405 0.057 - 0.114: 407 0.114 - 0.171: 65 0.171 - 0.228: 4 0.228 - 0.285: 1 Chirality restraints: 1882 Sorted by residual: chirality pdb=" CA ASN C 217 " pdb=" N ASN C 217 " pdb=" C ASN C 217 " pdb=" CB ASN C 217 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA ILE B 397 " pdb=" N ILE B 397 " pdb=" C ILE B 397 " pdb=" CB ILE B 397 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CA ILE L 23 " pdb=" N ILE L 23 " pdb=" C ILE L 23 " pdb=" CB ILE L 23 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.01e-01 ... (remaining 1879 not shown) Planarity restraints: 2008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN H 106 " -0.049 5.00e-02 4.00e+02 7.51e-02 9.01e+00 pdb=" N PRO H 107 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO H 107 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 107 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 71 " 0.030 2.00e-02 2.50e+03 1.85e-02 6.87e+00 pdb=" CG TYR C 71 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR C 71 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR C 71 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 71 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 71 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 71 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 71 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 184 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO B 185 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 185 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 185 " -0.033 5.00e-02 4.00e+02 ... (remaining 2005 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 173 2.61 - 3.18: 11225 3.18 - 3.76: 16719 3.76 - 4.33: 22617 4.33 - 4.90: 35791 Nonbonded interactions: 86525 Sorted by model distance: nonbonded pdb=" O TYR L 51 " pdb=" OG1 THR L 55 " model vdw 2.041 2.440 nonbonded pdb=" OG1 THR A 413 " pdb=" OE1 GLU A 416 " model vdw 2.047 2.440 nonbonded pdb=" O ALA B 150 " pdb=" OG1 THR B 154 " model vdw 2.070 2.440 nonbonded pdb=" OE2 GLU C 193 " pdb=" OG1 THR L 95 " model vdw 2.101 2.440 nonbonded pdb=" O LYS A 173 " pdb=" OH TYR A 235 " model vdw 2.155 2.440 ... (remaining 86520 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 20 through 84 or resid 124 through 215 or resid 226 throug \ h 260 or resid 263 through 472)) selection = (chain 'B' and (resid 20 through 84 or resid 124 through 472)) selection = (chain 'C' and (resid 20 through 215 or resid 226 through 260 or resid 263 throu \ gh 462 or (resid 463 and (name N or name CA or name C or name O or name CB )) or \ resid 464 through 472)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 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: 7.180 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 32.320 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5635 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 : 0.007 0.094 11618 Z= 0.483 Angle : 1.015 9.447 15769 Z= 0.556 Chirality : 0.052 0.285 1882 Planarity : 0.006 0.075 2008 Dihedral : 11.746 80.819 4302 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.27 % Allowed : 14.41 % Favored : 85.31 % Rotamer: Outliers : 0.38 % Allowed : 4.28 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -5.04 (0.18), residues: 1457 helix: -2.05 (0.22), residues: 359 sheet: -3.50 (0.32), residues: 180 loop : -4.12 (0.17), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 308 HIS 0.013 0.004 HIS L 91 PHE 0.033 0.003 PHE C 214 TYR 0.042 0.004 TYR C 71 ARG 0.013 0.002 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 332 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.5913 (mt) cc_final: 0.5659 (mt) REVERT: B 72 LYS cc_start: 0.6970 (mttt) cc_final: 0.6270 (mttt) REVERT: B 143 ASP cc_start: 0.5069 (m-30) cc_final: 0.4849 (m-30) REVERT: B 183 ILE cc_start: 0.8453 (tp) cc_final: 0.8221 (tp) REVERT: B 267 ILE cc_start: 0.5767 (pt) cc_final: 0.4754 (pt) REVERT: C 44 PHE cc_start: 0.4768 (t80) cc_final: 0.4537 (t80) REVERT: C 258 PHE cc_start: 0.6297 (t80) cc_final: 0.5829 (t80) outliers start: 5 outliers final: 1 residues processed: 337 average time/residue: 0.3047 time to fit residues: 136.2677 Evaluate side-chains 138 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.5980 chunk 109 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 113 optimal weight: 0.0470 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 131 optimal weight: 0.4980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 198 GLN A 386 ASN A 414 HIS B 26 GLN B 27 HIS B 198 GLN B 206 HIS B 362 GLN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN B 461 ASN C 43 ASN C 205 GLN ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN C 447 ASN H 5 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5901 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11618 Z= 0.225 Angle : 0.767 10.223 15769 Z= 0.405 Chirality : 0.048 0.265 1882 Planarity : 0.006 0.073 2008 Dihedral : 7.347 44.968 1574 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.36 % Favored : 89.43 % Rotamer: Outliers : 0.31 % Allowed : 4.28 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -3.89 (0.20), residues: 1457 helix: -0.67 (0.26), residues: 374 sheet: -3.03 (0.31), residues: 198 loop : -3.55 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.006 0.001 HIS L 91 PHE 0.015 0.002 PHE B 346 TYR 0.039 0.002 TYR C 71 ARG 0.008 0.001 ARG L 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 225 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.5399 (t80) cc_final: 0.5092 (t80) REVERT: A 73 ARG cc_start: 0.5702 (ptp-110) cc_final: 0.5095 (mtt180) REVERT: A 317 MET cc_start: 0.3219 (ptm) cc_final: 0.2936 (ptm) REVERT: B 58 GLU cc_start: 0.6521 (mp0) cc_final: 0.6297 (mp0) REVERT: B 149 GLU cc_start: 0.6130 (mt-10) cc_final: 0.5809 (mt-10) REVERT: C 44 PHE cc_start: 0.4689 (t80) cc_final: 0.4401 (t80) REVERT: L 90 CYS cc_start: 0.5940 (p) cc_final: 0.4961 (p) outliers start: 4 outliers final: 1 residues processed: 227 average time/residue: 0.2732 time to fit residues: 85.6812 Evaluate side-chains 117 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 105 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN B 238 ASN B 403 GLN ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11618 Z= 0.261 Angle : 0.768 9.975 15769 Z= 0.400 Chirality : 0.049 0.399 1882 Planarity : 0.006 0.081 2008 Dihedral : 6.756 37.955 1574 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.05 % Favored : 88.81 % Rotamer: Outliers : 0.23 % Allowed : 4.28 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.53 (0.20), residues: 1457 helix: -0.39 (0.26), residues: 391 sheet: -2.40 (0.30), residues: 218 loop : -3.49 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.005 0.001 HIS A 27 PHE 0.028 0.002 PHE B 427 TYR 0.039 0.003 TYR C 71 ARG 0.008 0.001 ARG L 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.5884 (t80) cc_final: 0.5446 (t80) REVERT: A 255 ASP cc_start: 0.4634 (p0) cc_final: 0.4315 (p0) REVERT: B 352 MET cc_start: 0.6513 (ttm) cc_final: 0.6291 (ttp) REVERT: B 427 PHE cc_start: 0.5336 (m-80) cc_final: 0.4724 (m-10) REVERT: C 44 PHE cc_start: 0.5366 (t80) cc_final: 0.5045 (t80) REVERT: H 67 VAL cc_start: 0.8485 (p) cc_final: 0.8249 (m) REVERT: L 91 HIS cc_start: 0.7932 (OUTLIER) cc_final: 0.6712 (t70) outliers start: 3 outliers final: 1 residues processed: 190 average time/residue: 0.2417 time to fit residues: 65.3492 Evaluate side-chains 111 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 176 GLN A 386 ASN A 395 ASN C 217 ASN C 407 GLN H 77 GLN ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.6557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11618 Z= 0.222 Angle : 0.713 8.392 15769 Z= 0.371 Chirality : 0.046 0.238 1882 Planarity : 0.005 0.067 2008 Dihedral : 6.412 35.493 1574 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.71 % Favored : 89.16 % Rotamer: Outliers : 0.08 % Allowed : 4.89 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.06 (0.21), residues: 1457 helix: -0.06 (0.27), residues: 379 sheet: -2.11 (0.34), residues: 189 loop : -3.10 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 HIS 0.003 0.001 HIS C 350 PHE 0.012 0.002 PHE B 258 TYR 0.035 0.002 TYR C 71 ARG 0.010 0.001 ARG L 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.6231 (ttpt) cc_final: 0.6004 (ttpt) REVERT: A 255 ASP cc_start: 0.4511 (p0) cc_final: 0.4217 (p0) REVERT: B 352 MET cc_start: 0.6958 (ttm) cc_final: 0.6232 (ttp) REVERT: C 44 PHE cc_start: 0.5361 (t80) cc_final: 0.4952 (t80) REVERT: H 67 VAL cc_start: 0.8393 (p) cc_final: 0.8189 (m) REVERT: L 90 CYS cc_start: 0.5186 (p) cc_final: 0.4413 (p) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.2341 time to fit residues: 57.4111 Evaluate side-chains 107 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 0.6980 chunk 79 optimal weight: 0.0000 chunk 2 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN L 81 GLN L 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.7156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11618 Z= 0.190 Angle : 0.692 7.737 15769 Z= 0.360 Chirality : 0.047 0.210 1882 Planarity : 0.005 0.062 2008 Dihedral : 6.201 33.998 1574 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.71 % Favored : 89.16 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.89 (0.21), residues: 1457 helix: 0.01 (0.28), residues: 374 sheet: -1.96 (0.34), residues: 190 loop : -2.95 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 37 HIS 0.006 0.001 HIS C 27 PHE 0.010 0.001 PHE C 214 TYR 0.038 0.002 TYR C 71 ARG 0.010 0.001 ARG L 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.6323 (ttpt) cc_final: 0.5989 (ttpt) REVERT: A 255 ASP cc_start: 0.4400 (p0) cc_final: 0.4100 (p0) REVERT: B 198 GLN cc_start: 0.6787 (pp30) cc_final: 0.6225 (pp30) REVERT: B 352 MET cc_start: 0.7008 (ttm) cc_final: 0.6138 (ttp) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2413 time to fit residues: 54.2877 Evaluate side-chains 107 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.8178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11618 Z= 0.293 Angle : 0.759 12.524 15769 Z= 0.395 Chirality : 0.047 0.230 1882 Planarity : 0.005 0.070 2008 Dihedral : 6.436 34.731 1574 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.22 % Favored : 87.65 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.01 (0.20), residues: 1457 helix: -0.23 (0.27), residues: 371 sheet: -1.94 (0.33), residues: 201 loop : -2.98 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 308 HIS 0.009 0.002 HIS L 91 PHE 0.019 0.002 PHE A 378 TYR 0.038 0.002 TYR B 254 ARG 0.008 0.001 ARG L 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 GLN cc_start: 0.7257 (pp30) cc_final: 0.6995 (pp30) REVERT: C 301 TYR cc_start: 0.6757 (t80) cc_final: 0.6550 (t80) REVERT: H 6 GLU cc_start: 0.5984 (tm-30) cc_final: 0.5499 (tm-30) REVERT: H 97 ARG cc_start: 0.5469 (tmt170) cc_final: 0.5170 (ttt-90) REVERT: L 6 MET cc_start: 0.7815 (ppp) cc_final: 0.7321 (ppp) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2172 time to fit residues: 47.8459 Evaluate side-chains 96 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 0.0060 chunk 102 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 78 optimal weight: 0.2980 chunk 139 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN H 77 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.8485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11618 Z= 0.200 Angle : 0.700 8.787 15769 Z= 0.366 Chirality : 0.046 0.216 1882 Planarity : 0.005 0.067 2008 Dihedral : 6.183 33.163 1574 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.05 % Favored : 88.81 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.85 (0.21), residues: 1457 helix: -0.11 (0.27), residues: 369 sheet: -1.91 (0.32), residues: 226 loop : -2.85 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 103 HIS 0.006 0.001 HIS L 91 PHE 0.026 0.002 PHE C 346 TYR 0.046 0.002 TYR C 71 ARG 0.011 0.001 ARG L 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 GLN cc_start: 0.7151 (pp30) cc_final: 0.6772 (pp30) REVERT: B 199 LEU cc_start: 0.8261 (pp) cc_final: 0.7933 (pp) REVERT: B 352 MET cc_start: 0.6335 (ttp) cc_final: 0.5926 (ttp) REVERT: C 209 GLU cc_start: 0.7334 (pm20) cc_final: 0.6929 (pm20) REVERT: H 6 GLU cc_start: 0.5686 (tm-30) cc_final: 0.5327 (tm-30) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2319 time to fit residues: 49.3110 Evaluate side-chains 103 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 88 optimal weight: 0.0370 chunk 95 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.8843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11618 Z= 0.202 Angle : 0.703 9.271 15769 Z= 0.365 Chirality : 0.046 0.224 1882 Planarity : 0.005 0.065 2008 Dihedral : 6.109 32.801 1574 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.46 % Favored : 88.40 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.77 (0.21), residues: 1457 helix: -0.01 (0.28), residues: 360 sheet: -1.89 (0.34), residues: 210 loop : -2.77 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 103 HIS 0.008 0.001 HIS C 27 PHE 0.029 0.002 PHE C 44 TYR 0.034 0.002 TYR H 59 ARG 0.012 0.001 ARG L 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.6233 (ttt) cc_final: 0.5998 (ttt) REVERT: B 198 GLN cc_start: 0.7165 (pp30) cc_final: 0.6873 (pp30) REVERT: B 199 LEU cc_start: 0.8293 (pp) cc_final: 0.7937 (pp) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2194 time to fit residues: 47.6668 Evaluate side-chains 101 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 56 optimal weight: 0.1980 chunk 102 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 117 optimal weight: 0.2980 chunk 123 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.9179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11618 Z= 0.204 Angle : 0.711 8.403 15769 Z= 0.368 Chirality : 0.046 0.232 1882 Planarity : 0.005 0.064 2008 Dihedral : 6.037 31.762 1574 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.84 % Favored : 89.09 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.72 (0.21), residues: 1457 helix: -0.04 (0.28), residues: 367 sheet: -1.68 (0.34), residues: 209 loop : -2.78 (0.19), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP L 37 HIS 0.007 0.001 HIS C 27 PHE 0.014 0.001 PHE A 378 TYR 0.030 0.002 TYR H 59 ARG 0.013 0.001 ARG L 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 GLN cc_start: 0.7203 (pp30) cc_final: 0.6932 (pp30) REVERT: B 199 LEU cc_start: 0.8300 (pp) cc_final: 0.7993 (pp) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2394 time to fit residues: 51.0094 Evaluate side-chains 100 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 0.0670 chunk 91 optimal weight: 3.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN L 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.9429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11618 Z= 0.205 Angle : 0.702 8.163 15769 Z= 0.363 Chirality : 0.046 0.192 1882 Planarity : 0.005 0.064 2008 Dihedral : 5.920 31.631 1574 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.32 % Favored : 88.61 % Rotamer: Outliers : 0.08 % Allowed : 0.69 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.67 (0.21), residues: 1457 helix: -0.04 (0.27), residues: 369 sheet: -1.57 (0.35), residues: 209 loop : -2.76 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP L 37 HIS 0.007 0.001 HIS C 27 PHE 0.018 0.002 PHE B 243 TYR 0.032 0.002 TYR C 71 ARG 0.015 0.001 ARG L 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 MET cc_start: 0.7863 (tpt) cc_final: 0.7159 (tpt) REVERT: B 198 GLN cc_start: 0.7190 (pp30) cc_final: 0.6941 (pp30) REVERT: B 199 LEU cc_start: 0.8340 (pp) cc_final: 0.8038 (pp) REVERT: L 6 MET cc_start: 0.7351 (ppp) cc_final: 0.6799 (ppp) REVERT: L 85 PHE cc_start: 0.6793 (t80) cc_final: 0.6589 (t80) outliers start: 1 outliers final: 1 residues processed: 140 average time/residue: 0.2356 time to fit residues: 48.0787 Evaluate side-chains 105 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.097744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.087977 restraints weight = 42142.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.089748 restraints weight = 28259.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.091039 restraints weight = 20513.995| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.9791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11618 Z= 0.219 Angle : 0.709 7.931 15769 Z= 0.370 Chirality : 0.046 0.190 1882 Planarity : 0.005 0.064 2008 Dihedral : 5.981 31.721 1574 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.19 % Favored : 88.68 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.68 (0.21), residues: 1457 helix: -0.17 (0.27), residues: 372 sheet: -1.50 (0.35), residues: 210 loop : -2.73 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 37 HIS 0.007 0.002 HIS C 27 PHE 0.014 0.002 PHE A 378 TYR 0.030 0.002 TYR B 254 ARG 0.014 0.001 ARG L 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2378.27 seconds wall clock time: 44 minutes 38.55 seconds (2678.55 seconds total)