Starting phenix.real_space_refine on Mon Dec 30 00:12:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9axl_43969/12_2024/9axl_43969_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9axl_43969/12_2024/9axl_43969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9axl_43969/12_2024/9axl_43969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9axl_43969/12_2024/9axl_43969.map" model { file = "/net/cci-nas-00/data/ceres_data/9axl_43969/12_2024/9axl_43969_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9axl_43969/12_2024/9axl_43969_neut.cif" } resolution = 3.3 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= 0.000 sd= 0.087 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 Mg 1 5.21 5 S 72 5.16 5 C 7355 2.51 5 N 2009 2.21 5 O 2305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11748 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4514 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 591, 4484 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 36, 'TRANS': 554} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 591, 4484 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 36, 'TRANS': 554} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 4561 Chain: "B" Number of atoms: 3885 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 524, 3881 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 494} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Conformer: "B" Number of residues, atoms: 524, 3881 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 494} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 bond proxies already assigned to first conformer: 3942 Chain: "H" Number of atoms: 1698 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1681 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 213} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 227, 1681 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 213} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 1706 Chain: "L" Number of atoms: 1637 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 213, 1637 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 201} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3, 'water': 7} Link IDs: {None: 9} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG A 276 " occ=0.73 ... (20 atoms not shown) pdb=" NH2BARG A 276 " occ=0.27 residue: pdb=" N AHIS A 587 " occ=0.67 ... (18 atoms not shown) pdb=" NE2BHIS A 587 " occ=0.33 residue: pdb=" N AARG H 98 " occ=0.43 ... (20 atoms not shown) pdb=" NH2BARG H 98 " occ=0.57 residue: pdb=" N CYS L 213 " occ=0.00 ... (5 atoms not shown) pdb=" OXT CYS L 213 " occ=0.00 Time building chain proxies: 12.44, per 1000 atoms: 1.06 Number of scatterers: 11748 At special positions: 0 Unit cell: (86, 105.78, 190.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 72 16.00 Mg 1 11.99 O 2305 8.00 N 2009 7.00 C 7355 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.02 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 435 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 38 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.04 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 460 " distance=2.03 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 471 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 503 " distance=2.03 Simple disulfide: pdb=" SG CYS B 508 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS L 213 " distance=2.03 Simple disulfide: pdb=" SG CYS H 152 " - pdb=" SG CYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG ACYS L 193 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 3.06 Conformation dependent library (CDL) restraints added in 3.0 seconds 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2866 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 30 sheets defined 12.6% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.723A pdb=" N TYR A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 259 through 264 removed outlier: 4.048A pdb=" N THR A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.692A pdb=" N ARG A 519 " --> pdb=" O ARG A 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 8 removed outlier: 3.888A pdb=" N ARG B 8 " --> pdb=" O CYS B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 20 removed outlier: 4.483A pdb=" N SER B 20 " --> pdb=" O CYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 121 through 130 removed outlier: 5.280A pdb=" N ASP B 126 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP B 127 " --> pdb=" O MET B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 142 removed outlier: 3.698A pdb=" N LYS B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 141 " --> pdb=" O LYS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 165 Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.585A pdb=" N LEU B 173 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 208 removed outlier: 3.961A pdb=" N ASN B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 281 through 286 removed outlier: 3.654A pdb=" N SER B 284 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 302 Processing helix chain 'B' and resid 312 through 323 removed outlier: 4.632A pdb=" N ASN B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B 317 " --> pdb=" O ASN B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 354 removed outlier: 3.926A pdb=" N LYS B 354 " --> pdb=" O LYS B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 439 removed outlier: 3.587A pdb=" N ALA B 439 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 497 removed outlier: 3.648A pdb=" N SER B 496 " --> pdb=" O PRO B 493 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 68 Processing helix chain 'H' and resid 168 through 170 No H-bonds generated for 'chain 'H' and resid 168 through 170' Processing helix chain 'L' and resid 120 through 127 Processing helix chain 'L' and resid 182 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 3.564A pdb=" N THR A 9 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER A 420 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 79 removed outlier: 3.500A pdb=" N GLU A 75 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 100 removed outlier: 3.831A pdb=" N SER A 96 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 175 removed outlier: 3.804A pdb=" N SER A 172 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.662A pdb=" N HIS A 278 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 296 removed outlier: 3.542A pdb=" N LEU A 345 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 364 removed outlier: 6.165A pdb=" N ASP A 373 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AB2, first strand: chain 'A' and resid 522 through 523 removed outlier: 5.322A pdb=" N VAL A 454 " --> pdb=" O AHIS A 587 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 530 through 536 Processing sheet with id=AB5, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AB6, first strand: chain 'B' and resid 60 through 65 removed outlier: 6.236A pdb=" N ARG B 87 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.681A pdb=" N ALA B 372 " --> pdb=" O ILE B 380 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 194 through 197 removed outlier: 3.680A pdb=" N LEU B 194 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU B 196 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE B 151 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR B 116 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR B 250 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 311 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N THR B 329 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 306 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLY B 331 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE B 308 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU B 333 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL B 310 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 454 through 456 removed outlier: 3.533A pdb=" N GLU B 456 " --> pdb=" O VAL B 459 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 466 through 467 removed outlier: 3.834A pdb=" N CYS B 473 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 499 through 501 Processing sheet with id=AC3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.697A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.171A pdb=" N TYR H 187 " --> pdb=" O GLY H 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.171A pdb=" N TYR H 187 " --> pdb=" O GLY H 156 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 165 through 166 removed outlier: 3.678A pdb=" N THR H 165 " --> pdb=" O ASN H 208 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.666A pdb=" N THR L 5 " --> pdb=" O SER L 24 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER L 69 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER L 66 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.615A pdb=" N ALA L 13 " --> pdb=" O GLU L 104 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AD2, first strand: chain 'L' and resid 113 through 117 removed outlier: 5.893A pdb=" N TYR L 172 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 144 through 149 411 hydrogen bonds defined for protein. 1034 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: 4.03 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.19: 1 1.19 - 1.52: 10305 1.52 - 1.86: 1696 1.86 - 2.20: 0 2.20 - 2.54: 1 Bond restraints: 12003 Sorted by residual: bond pdb=" CB PRO B 363 " pdb=" CG PRO B 363 " ideal model delta sigma weight residual 1.492 2.539 -1.047 5.00e-02 4.00e+02 4.39e+02 bond pdb=" CG PRO B 363 " pdb=" CD PRO B 363 " ideal model delta sigma weight residual 1.503 0.849 0.654 3.40e-02 8.65e+02 3.70e+02 bond pdb=" N PRO B 363 " pdb=" CD PRO B 363 " ideal model delta sigma weight residual 1.473 1.574 -0.101 1.40e-02 5.10e+03 5.16e+01 bond pdb=" CA PRO B 363 " pdb=" CB PRO B 363 " ideal model delta sigma weight residual 1.535 1.437 0.099 1.60e-02 3.91e+03 3.81e+01 bond pdb=" N PRO B 363 " pdb=" CA PRO B 363 " ideal model delta sigma weight residual 1.464 1.419 0.044 9.30e-03 1.16e+04 2.27e+01 ... (remaining 11998 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.86: 16339 15.86 - 31.72: 3 31.72 - 47.58: 0 47.58 - 63.44: 0 63.44 - 79.30: 1 Bond angle restraints: 16343 Sorted by residual: angle pdb=" CB PRO B 363 " pdb=" CG PRO B 363 " pdb=" CD PRO B 363 " ideal model delta sigma weight residual 106.10 26.80 79.30 3.20e+00 9.77e-02 6.14e+02 angle pdb=" CA PRO B 363 " pdb=" CB PRO B 363 " pdb=" CG PRO B 363 " ideal model delta sigma weight residual 104.50 76.10 28.40 1.90e+00 2.77e-01 2.23e+02 angle pdb=" N PRO B 363 " pdb=" CD PRO B 363 " pdb=" CG PRO B 363 " ideal model delta sigma weight residual 103.20 82.68 20.52 1.50e+00 4.44e-01 1.87e+02 angle pdb=" N PRO B 363 " pdb=" CA PRO B 363 " pdb=" CB PRO B 363 " ideal model delta sigma weight residual 102.72 89.52 13.20 1.16e+00 7.43e-01 1.29e+02 angle pdb=" CA PRO B 363 " pdb=" N PRO B 363 " pdb=" CD PRO B 363 " ideal model delta sigma weight residual 112.00 97.83 14.17 1.40e+00 5.10e-01 1.02e+02 ... (remaining 16338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.83: 6612 22.83 - 45.67: 515 45.67 - 68.50: 83 68.50 - 91.33: 16 91.33 - 114.17: 1 Dihedral angle restraints: 7227 sinusoidal: 2740 harmonic: 4487 Sorted by residual: dihedral pdb=" CA LYS L 93 " pdb=" C LYS L 93 " pdb=" N PRO L 94 " pdb=" CA PRO L 94 " ideal model delta harmonic sigma weight residual 180.00 126.09 53.91 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" CB CYS B 374 " pdb=" SG CYS B 374 " pdb=" SG CYS B 386 " pdb=" CB CYS B 386 " ideal model delta sinusoidal sigma weight residual 93.00 -176.68 -90.32 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS B 13 " pdb=" SG CYS B 13 " pdb=" SG CYS B 435 " pdb=" CB CYS B 435 " ideal model delta sinusoidal sigma weight residual 93.00 -177.93 -89.07 1 1.00e+01 1.00e-02 9.44e+01 ... (remaining 7224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1444 0.057 - 0.113: 325 0.113 - 0.170: 51 0.170 - 0.226: 1 0.226 - 0.283: 2 Chirality restraints: 1823 Sorted by residual: chirality pdb=" CA PRO B 363 " pdb=" N PRO B 363 " pdb=" C PRO B 363 " pdb=" CB PRO B 363 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA PRO B 443 " pdb=" N PRO B 443 " pdb=" C PRO B 443 " pdb=" CB PRO B 443 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ASP A 245 " pdb=" N ASP A 245 " pdb=" C ASP A 245 " pdb=" CB ASP A 245 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.34e-01 ... (remaining 1820 not shown) Planarity restraints: 2139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 93 " 0.073 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO B 94 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO B 94 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 94 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 158 " -0.061 5.00e-02 4.00e+02 9.36e-02 1.40e+01 pdb=" N PRO H 159 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 33 " 0.015 2.00e-02 2.50e+03 2.12e-02 1.13e+01 pdb=" CG TRP H 33 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP H 33 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP H 33 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 33 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP H 33 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP H 33 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 33 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 33 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP H 33 " 0.004 2.00e-02 2.50e+03 ... (remaining 2136 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 96 2.54 - 3.13: 8515 3.13 - 3.72: 16871 3.72 - 4.31: 23652 4.31 - 4.90: 42143 Nonbonded interactions: 91277 Sorted by model distance: nonbonded pdb="MG MG B1002 " pdb=" O HOH B1101 " model vdw 1.949 2.170 nonbonded pdb="MG MG B1002 " pdb=" O HOH B1102 " model vdw 1.953 2.170 nonbonded pdb=" OD1 ASP B 217 " pdb="CA CA B1001 " model vdw 2.098 2.510 nonbonded pdb=" OD2 ASP B 158 " pdb="CA CA B1001 " model vdw 2.158 2.510 nonbonded pdb=" ND2 ASN B 215 " pdb="CA CA B1001 " model vdw 2.170 2.590 ... (remaining 91272 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.710 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: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 37.320 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.047 12003 Z= 0.999 Angle : 1.019 79.302 16343 Z= 0.489 Chirality : 0.049 0.283 1823 Planarity : 0.006 0.106 2139 Dihedral : 16.021 114.166 4298 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.31 % Favored : 92.43 % Rotamer: Outliers : 0.55 % Allowed : 20.41 % Favored : 79.03 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 3.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.21), residues: 1559 helix: -1.36 (0.42), residues: 127 sheet: -0.02 (0.23), residues: 582 loop : -1.52 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP H 33 HIS 0.006 0.001 HIS B 192 PHE 0.019 0.002 PHE B 308 TYR 0.019 0.002 TYR H 109 ARG 0.005 0.001 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 1.349 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 104 average time/residue: 0.2729 time to fit residues: 41.0498 Evaluate side-chains 100 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 20.0000 chunk 116 optimal weight: 0.4980 chunk 64 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 46 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 12003 Z= 0.217 Angle : 0.600 13.002 16343 Z= 0.309 Chirality : 0.044 0.142 1823 Planarity : 0.005 0.087 2139 Dihedral : 4.562 51.989 1683 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.83 % Favored : 93.98 % Rotamer: Outliers : 1.98 % Allowed : 19.15 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 3.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.21), residues: 1559 helix: -0.73 (0.43), residues: 128 sheet: 0.14 (0.23), residues: 585 loop : -1.34 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 33 HIS 0.003 0.001 HIS B 280 PHE 0.012 0.001 PHE A 19 TYR 0.017 0.001 TYR H 27 ARG 0.004 0.000 ARG B 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.7995 (t80) REVERT: B 74 SER cc_start: 0.7642 (t) cc_final: 0.7058 (p) REVERT: B 207 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8841 (p) outliers start: 20 outliers final: 12 residues processed: 126 average time/residue: 0.2444 time to fit residues: 45.1986 Evaluate side-chains 118 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain L residue 62 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 151 optimal weight: 40.0000 chunk 124 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 112 optimal weight: 0.0040 overall best weight: 1.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 12003 Z= 0.467 Angle : 0.710 14.916 16343 Z= 0.364 Chirality : 0.050 0.191 1823 Planarity : 0.006 0.087 2139 Dihedral : 5.082 53.890 1683 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.90 % Favored : 91.78 % Rotamer: Outliers : 2.77 % Allowed : 18.43 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 3.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.21), residues: 1559 helix: -1.02 (0.42), residues: 128 sheet: -0.03 (0.23), residues: 583 loop : -1.55 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 33 HIS 0.006 0.001 HIS A 291 PHE 0.020 0.003 PHE A 19 TYR 0.020 0.002 TYR H 27 ARG 0.004 0.001 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9187 (OUTLIER) cc_final: 0.8216 (t80) outliers start: 30 outliers final: 20 residues processed: 124 average time/residue: 0.2420 time to fit residues: 44.2576 Evaluate side-chains 121 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain L residue 62 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 15 optimal weight: 0.0670 chunk 66 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 148 optimal weight: 30.0000 chunk 73 optimal weight: 0.0010 chunk 133 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 overall best weight: 0.5124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12003 Z= 0.187 Angle : 0.568 13.733 16343 Z= 0.291 Chirality : 0.044 0.145 1823 Planarity : 0.005 0.083 2139 Dihedral : 4.599 51.803 1683 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.15 % Favored : 93.59 % Rotamer: Outliers : 2.14 % Allowed : 19.22 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 3.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.21), residues: 1559 helix: -0.63 (0.44), residues: 129 sheet: 0.11 (0.23), residues: 584 loop : -1.33 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 33 HIS 0.003 0.001 HIS B 192 PHE 0.019 0.001 PHE B 455 TYR 0.016 0.001 TYR H 27 ARG 0.003 0.000 ARG B 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.8074 (t80) REVERT: B 207 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8864 (p) outliers start: 22 outliers final: 17 residues processed: 128 average time/residue: 0.2331 time to fit residues: 43.8667 Evaluate side-chains 122 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain L residue 62 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 110 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 102 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12003 Z= 0.210 Angle : 0.568 13.383 16343 Z= 0.290 Chirality : 0.044 0.157 1823 Planarity : 0.005 0.082 2139 Dihedral : 4.499 51.570 1683 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.34 % Favored : 93.33 % Rotamer: Outliers : 2.77 % Allowed : 18.99 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 2.25 % 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: 1559 helix: -0.45 (0.44), residues: 129 sheet: 0.19 (0.23), residues: 574 loop : -1.25 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 33 HIS 0.003 0.001 HIS B 192 PHE 0.024 0.002 PHE B 455 TYR 0.020 0.001 TYR H 60 ARG 0.002 0.000 ARG B 447 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 1.282 Fit side-chains REVERT: A 288 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.7994 (t80) REVERT: A 365 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7998 (m-30) REVERT: B 74 SER cc_start: 0.7661 (t) cc_final: 0.7046 (p) REVERT: B 207 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8851 (p) outliers start: 30 outliers final: 22 residues processed: 132 average time/residue: 0.2380 time to fit residues: 46.3944 Evaluate side-chains 130 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain L residue 62 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 5.9990 chunk 134 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.0770 chunk 78 optimal weight: 1.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12003 Z= 0.245 Angle : 0.584 13.705 16343 Z= 0.298 Chirality : 0.045 0.157 1823 Planarity : 0.005 0.080 2139 Dihedral : 4.550 52.062 1683 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.54 % Favored : 93.20 % Rotamer: Outliers : 2.53 % Allowed : 19.62 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 2.25 % 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: -0.96 (0.21), residues: 1559 helix: -0.47 (0.44), residues: 129 sheet: 0.18 (0.23), residues: 585 loop : -1.26 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 33 HIS 0.004 0.001 HIS B 192 PHE 0.019 0.002 PHE B 455 TYR 0.037 0.002 TYR H 109 ARG 0.002 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 1.312 Fit side-chains REVERT: A 288 TYR cc_start: 0.9096 (OUTLIER) cc_final: 0.8029 (t80) REVERT: A 365 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8027 (m-30) REVERT: B 74 SER cc_start: 0.7581 (t) cc_final: 0.7003 (p) REVERT: B 207 VAL cc_start: 0.9157 (OUTLIER) cc_final: 0.8856 (p) outliers start: 27 outliers final: 21 residues processed: 132 average time/residue: 0.2442 time to fit residues: 47.9589 Evaluate side-chains 131 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 77 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 125 optimal weight: 0.0670 chunk 83 optimal weight: 1.9990 chunk 148 optimal weight: 40.0000 chunk 92 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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: 0.7660 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12003 Z= 0.187 Angle : 0.547 12.828 16343 Z= 0.280 Chirality : 0.044 0.152 1823 Planarity : 0.005 0.079 2139 Dihedral : 4.360 50.686 1683 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.08 % Favored : 93.72 % Rotamer: Outliers : 2.77 % Allowed : 19.54 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 2.25 % 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: 1559 helix: -0.26 (0.45), residues: 128 sheet: 0.31 (0.23), residues: 579 loop : -1.21 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 47 HIS 0.003 0.001 HIS B 192 PHE 0.010 0.001 PHE A 19 TYR 0.023 0.001 TYR H 109 ARG 0.002 0.000 ARG B 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 1.320 Fit side-chains REVERT: A 288 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.8051 (t80) REVERT: A 365 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.8022 (m-30) REVERT: B 74 SER cc_start: 0.7631 (t) cc_final: 0.7097 (p) REVERT: B 180 MET cc_start: 0.7307 (mtt) cc_final: 0.6948 (mtt) REVERT: B 207 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8850 (p) outliers start: 29 outliers final: 20 residues processed: 131 average time/residue: 0.2452 time to fit residues: 47.5516 Evaluate side-chains 121 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 99 TRP Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 77 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 8.9990 chunk 88 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 116 optimal weight: 0.0980 chunk 135 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.7710 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12003 Z= 0.286 Angle : 0.601 13.914 16343 Z= 0.307 Chirality : 0.046 0.165 1823 Planarity : 0.005 0.082 2139 Dihedral : 4.585 52.366 1683 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.06 % Favored : 92.69 % Rotamer: Outliers : 2.77 % Allowed : 19.54 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 2.25 % 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: -0.91 (0.21), residues: 1559 helix: -0.43 (0.45), residues: 128 sheet: 0.23 (0.23), residues: 583 loop : -1.25 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.004 0.001 HIS B 192 PHE 0.014 0.002 PHE A 19 TYR 0.025 0.002 TYR H 109 ARG 0.002 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 1.270 Fit side-chains REVERT: A 288 TYR cc_start: 0.9129 (OUTLIER) cc_final: 0.8074 (t80) REVERT: A 365 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.7987 (m-30) REVERT: B 74 SER cc_start: 0.7641 (t) cc_final: 0.7095 (p) REVERT: B 180 MET cc_start: 0.7418 (mtt) cc_final: 0.7067 (mtt) REVERT: B 207 VAL cc_start: 0.9173 (OUTLIER) cc_final: 0.8871 (p) REVERT: B 233 ASP cc_start: 0.7548 (m-30) cc_final: 0.7336 (m-30) REVERT: B 515 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6800 (mttp) outliers start: 29 outliers final: 23 residues processed: 127 average time/residue: 0.2520 time to fit residues: 46.6445 Evaluate side-chains 128 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 99 TRP Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 77 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 0.9990 chunk 129 optimal weight: 0.0770 chunk 138 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 130 optimal weight: 30.0000 chunk 137 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 overall best weight: 0.6942 ------------------------------------------------------------------------------- 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: 0.7680 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12003 Z= 0.211 Angle : 0.567 13.496 16343 Z= 0.289 Chirality : 0.044 0.152 1823 Planarity : 0.005 0.083 2139 Dihedral : 4.460 51.469 1683 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.28 % Favored : 93.53 % Rotamer: Outliers : 2.77 % Allowed : 19.62 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 2.25 % 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: -0.79 (0.22), residues: 1559 helix: -0.35 (0.45), residues: 128 sheet: 0.29 (0.22), residues: 606 loop : -1.18 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 33 HIS 0.003 0.001 HIS B 192 PHE 0.015 0.001 PHE B 455 TYR 0.023 0.001 TYR H 109 ARG 0.002 0.000 ARG B 447 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 1.211 Fit side-chains REVERT: A 288 TYR cc_start: 0.9065 (OUTLIER) cc_final: 0.7977 (t80) REVERT: A 365 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8028 (m-30) REVERT: B 74 SER cc_start: 0.7603 (t) cc_final: 0.7104 (p) REVERT: B 180 MET cc_start: 0.7392 (mtt) cc_final: 0.7169 (mtt) REVERT: B 207 VAL cc_start: 0.9153 (OUTLIER) cc_final: 0.8857 (p) outliers start: 29 outliers final: 22 residues processed: 124 average time/residue: 0.2437 time to fit residues: 44.6220 Evaluate side-chains 126 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 77 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 101 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 12 optimal weight: 0.0270 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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: 0.7666 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12003 Z= 0.197 Angle : 0.553 13.318 16343 Z= 0.282 Chirality : 0.044 0.148 1823 Planarity : 0.005 0.082 2139 Dihedral : 4.366 51.185 1683 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.41 % Favored : 93.40 % Rotamer: Outliers : 2.85 % Allowed : 19.62 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 2.25 % 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: -0.70 (0.22), residues: 1559 helix: -0.26 (0.45), residues: 128 sheet: 0.35 (0.22), residues: 606 loop : -1.12 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE B 455 TYR 0.019 0.001 TYR H 109 ARG 0.002 0.000 ARG B 461 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 1.197 Fit side-chains REVERT: A 288 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.8072 (t80) REVERT: A 365 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.8023 (m-30) REVERT: B 74 SER cc_start: 0.7531 (t) cc_final: 0.7072 (p) REVERT: B 207 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8857 (p) outliers start: 30 outliers final: 23 residues processed: 127 average time/residue: 0.2451 time to fit residues: 45.5761 Evaluate side-chains 126 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 77 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 7.9990 chunk 37 optimal weight: 0.0470 chunk 112 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 15 optimal weight: 0.0870 chunk 22 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.214276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.156528 restraints weight = 42884.059| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 8.86 r_work: 0.3214 rms_B_bonded: 7.63 restraints_weight: 2.0000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12003 Z= 0.152 Angle : 0.528 12.068 16343 Z= 0.270 Chirality : 0.043 0.140 1823 Planarity : 0.005 0.081 2139 Dihedral : 4.199 49.786 1683 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.37 % Favored : 94.43 % Rotamer: Outliers : 2.14 % Allowed : 20.33 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 2.25 % 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: -0.53 (0.22), residues: 1559 helix: -0.08 (0.46), residues: 128 sheet: 0.57 (0.23), residues: 586 loop : -1.08 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 99 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.001 PHE B 248 TYR 0.021 0.001 TYR H 109 ARG 0.002 0.000 ARG B 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2554.58 seconds wall clock time: 48 minutes 0.43 seconds (2880.43 seconds total)