Starting phenix.real_space_refine on Mon Sep 23 20:53:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctg_26989/09_2024/8ctg_26989.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctg_26989/09_2024/8ctg_26989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctg_26989/09_2024/8ctg_26989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctg_26989/09_2024/8ctg_26989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctg_26989/09_2024/8ctg_26989.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctg_26989/09_2024/8ctg_26989.cif" } resolution = 3.8 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= 0.002 sd= 0.035 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 45 5.16 5 C 3041 2.51 5 N 1006 2.21 5 O 1008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5100 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 618 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 105} Unresolved non-hydrogen bonds: 343 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 7, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 222 Chain: "B" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1585 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 241} Link IDs: {'PTRANS': 4, 'TRANS': 311} Unresolved non-hydrogen bonds: 908 Unresolved non-hydrogen angles: 1156 Unresolved non-hydrogen dihedrals: 769 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 14, 'TYR:plan': 5, 'ASN:plan1': 18, 'TRP:plan': 8, 'HIS:plan': 8, 'PHE:plan': 11, 'GLU:plan': 21, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 541 Chain: "C" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 2880 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 456} Link IDs: {'PTRANS': 24, 'TRANS': 547} Chain breaks: 3 Unresolved non-hydrogen bonds: 1778 Unresolved non-hydrogen angles: 2320 Unresolved non-hydrogen dihedrals: 1490 Unresolved non-hydrogen chiralities: 166 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 12, 'TYR:plan': 21, 'ASN:plan1': 22, 'TRP:plan': 19, 'ASP:plan': 51, 'PHE:plan': 17, 'GLU:plan': 35, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 1084 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PAM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PAM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 69 residue: pdb=" N LEU A 97 " occ=0.20 ... (3 atoms not shown) pdb=" CB LEU A 97 " occ=0.20 residue: pdb=" N GLU A 98 " occ=0.20 ... (3 atoms not shown) pdb=" CB GLU A 98 " occ=0.20 residue: pdb=" N ASP A 99 " occ=0.20 ... (3 atoms not shown) pdb=" CB ASP A 99 " occ=0.20 residue: pdb=" N TYR A 100 " occ=0.20 ... (3 atoms not shown) pdb=" CB TYR A 100 " occ=0.20 residue: pdb=" N LYS A 101 " occ=0.20 ... (3 atoms not shown) pdb=" CB LYS A 101 " occ=0.20 residue: pdb=" N PRO B 67 " occ=0.20 ... (5 atoms not shown) pdb=" CD PRO B 67 " occ=0.20 residue: pdb=" N GLU B 68 " occ=0.20 ... (3 atoms not shown) pdb=" CB GLU B 68 " occ=0.20 residue: pdb=" N SER B 69 " occ=0.20 ... (3 atoms not shown) pdb=" CB SER B 69 " occ=0.20 residue: pdb=" N THR B 70 " occ=0.20 ... (3 atoms not shown) pdb=" CB THR B 70 " occ=0.20 residue: pdb=" N LEU B 71 " occ=0.20 ... (3 atoms not shown) pdb=" CB LEU B 71 " occ=0.20 residue: pdb=" N GLN B 72 " occ=0.20 ... (3 atoms not shown) pdb=" CB GLN B 72 " occ=0.20 residue: pdb=" N LEU B 73 " occ=0.20 ... (3 atoms not shown) pdb=" CB LEU B 73 " occ=0.20 ... (remaining 57 not shown) Time building chain proxies: 4.73, per 1000 atoms: 0.93 Number of scatterers: 5100 At special positions: 0 Unit cell: (69.0201, 97.9915, 134.632, 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 45 16.00 O 1008 8.00 N 1006 7.00 C 3041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 118 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 135 " distance=2.04 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 66 " distance=2.03 Simple disulfide: pdb=" SG CYS B 105 " - pdb=" SG CYS B 113 " distance=2.03 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 181 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 190 " distance=2.03 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 298 " distance=2.04 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 328 " distance=2.02 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 325 " distance=2.03 Simple disulfide: pdb=" SG CYS B 320 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS C 286 " - pdb=" SG CYS C 297 " distance=2.03 Simple disulfide: pdb=" SG CYS C 293 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 323 " distance=2.03 Simple disulfide: pdb=" SG CYS C 592 " - pdb=" SG CYS C 603 " distance=2.04 Simple disulfide: pdb=" SG CYS C 599 " - pdb=" SG CYS C 612 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 1.0 seconds 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1862 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 19 sheets defined 22.1% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 61 through 70 Processing helix chain 'A' and resid 72 through 79 Processing helix chain 'A' and resid 81 through 93 removed outlier: 4.538A pdb=" N LYS A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE A 86 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 125 Proline residue: A 120 - end of helix Processing helix chain 'A' and resid 130 through 134 removed outlier: 3.511A pdb=" N ARG A 134 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 59 removed outlier: 3.581A pdb=" N SER B 41 " --> pdb=" O TYR B 37 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N SER B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 83 through 107 removed outlier: 3.789A pdb=" N SER B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE B 88 " --> pdb=" O ARG B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 115 removed outlier: 5.995A pdb=" N ASN B 112 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 152 removed outlier: 3.740A pdb=" N GLY B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 176 Processing helix chain 'B' and resid 185 through 189 Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.521A pdb=" N ILE B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 284 through 295 removed outlier: 4.118A pdb=" N CYS B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LYS B 292 " --> pdb=" O ARG B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 299 Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 289 through 293 Processing helix chain 'C' and resid 590 through 599 removed outlier: 4.417A pdb=" N GLU C 595 " --> pdb=" O CYS C 592 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASN C 596 " --> pdb=" O ALA C 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 Processing sheet with id=AA2, first strand: chain 'B' and resid 123 through 125 removed outlier: 6.479A pdb=" N ILE B 123 " --> pdb=" O TRP B 130 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TRP B 130 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B 125 " --> pdb=" O TRP B 128 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 129 " --> pdb=" O CYS B 195 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N LEU B 197 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 262 through 263 Processing sheet with id=AA4, first strand: chain 'B' and resid 275 through 276 Processing sheet with id=AA5, first strand: chain 'B' and resid 310 through 311 Processing sheet with id=AA6, first strand: chain 'C' and resid 31 through 34 removed outlier: 3.840A pdb=" N ARG C 32 " --> pdb=" O TYR C 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 59 removed outlier: 6.176A pdb=" N SER C 68 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL C 56 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR C 66 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE C 58 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU C 64 " --> pdb=" O PHE C 58 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE C 75 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 97 through 103 removed outlier: 3.647A pdb=" N GLY C 99 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 118 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE C 119 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 140 through 146 removed outlier: 4.665A pdb=" N ALA C 142 " --> pdb=" O THR C 155 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE C 163 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 184 through 190 removed outlier: 5.200A pdb=" N GLY C 186 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C 199 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 206 " --> pdb=" O GLN C 217 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 230 through 232 removed outlier: 3.669A pdb=" N THR C 231 " --> pdb=" O TYR C 238 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR C 238 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE C 247 " --> pdb=" O ILE C 261 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 296 through 299 Processing sheet with id=AB4, first strand: chain 'C' and resid 351 through 353 removed outlier: 3.539A pdb=" N ILE C 342 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU C 330 " --> pdb=" O THR C 581 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR C 581 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU C 332 " --> pdb=" O LYS C 579 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS C 579 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY C 577 " --> pdb=" O ALA C 334 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 362 through 368 removed outlier: 4.219A pdb=" N ALA C 364 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE C 384 " --> pdb=" O VAL C 397 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 407 through 411 removed outlier: 6.593A pdb=" N ILE C 427 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 448 through 454 removed outlier: 4.753A pdb=" N ALA C 450 " --> pdb=" O THR C 463 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE C 471 " --> pdb=" O LEU C 484 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 492 through 498 removed outlier: 3.532A pdb=" N GLY C 494 " --> pdb=" O GLY C 507 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS C 513 " --> pdb=" O ASP C 508 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE C 514 " --> pdb=" O LEU C 527 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 539 through 541 removed outlier: 3.657A pdb=" N TYR C 544 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG C 557 " --> pdb=" O VAL C 567 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N VAL C 567 " --> pdb=" O ARG C 557 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N HIS C 559 " --> pdb=" O ARG C 565 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARG C 565 " --> pdb=" O HIS C 559 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 602 through 606 286 hydrogen bonds defined for protein. 702 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: 1.99 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 1888 1.34 - 1.47: 1123 1.47 - 1.60: 2078 1.60 - 1.74: 0 1.74 - 1.87: 45 Bond restraints: 5134 Sorted by residual: bond pdb=" C LYS C 303 " pdb=" N PRO C 304 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.19e+00 bond pdb=" C1 PAM B 401 " pdb=" O1 PAM B 401 " ideal model delta sigma weight residual 1.250 1.202 0.048 2.00e-02 2.50e+03 5.86e+00 bond pdb=" CB CYS B 321 " pdb=" SG CYS B 321 " ideal model delta sigma weight residual 1.808 1.873 -0.065 3.30e-02 9.18e+02 3.88e+00 bond pdb=" CB SER B 187 " pdb=" OG SER B 187 " ideal model delta sigma weight residual 1.417 1.451 -0.034 2.00e-02 2.50e+03 2.82e+00 bond pdb=" C1 PAM B 401 " pdb=" C2 PAM B 401 " ideal model delta sigma weight residual 1.538 1.504 0.034 2.00e-02 2.50e+03 2.81e+00 ... (remaining 5129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 6606 1.70 - 3.40: 430 3.40 - 5.10: 84 5.10 - 6.80: 14 6.80 - 8.50: 4 Bond angle restraints: 7138 Sorted by residual: angle pdb=" C GLY B 114 " pdb=" N CYS B 115 " pdb=" CA CYS B 115 " ideal model delta sigma weight residual 121.54 129.52 -7.98 1.91e+00 2.74e-01 1.74e+01 angle pdb=" CA ARG C 141 " pdb=" C ARG C 141 " pdb=" N ALA C 142 " ideal model delta sigma weight residual 119.56 117.20 2.36 5.80e-01 2.97e+00 1.65e+01 angle pdb=" N VAL C 381 " pdb=" CA VAL C 381 " pdb=" C VAL C 381 " ideal model delta sigma weight residual 112.04 107.30 4.74 1.40e+00 5.10e-01 1.14e+01 angle pdb=" CA LYS C 303 " pdb=" C LYS C 303 " pdb=" N PRO C 304 " ideal model delta sigma weight residual 118.44 123.77 -5.33 1.59e+00 3.96e-01 1.12e+01 angle pdb=" N SER C 179 " pdb=" CA SER C 179 " pdb=" C SER C 179 " ideal model delta sigma weight residual 108.67 113.78 -5.11 1.55e+00 4.16e-01 1.09e+01 ... (remaining 7133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.04: 2980 12.04 - 24.08: 84 24.08 - 36.13: 23 36.13 - 48.17: 10 48.17 - 60.21: 10 Dihedral angle restraints: 3107 sinusoidal: 245 harmonic: 2862 Sorted by residual: dihedral pdb=" CB CYS B 313 " pdb=" SG CYS B 313 " pdb=" SG CYS B 328 " pdb=" CB CYS B 328 " ideal model delta sinusoidal sigma weight residual 93.00 37.41 55.59 1 1.00e+01 1.00e-02 4.17e+01 dihedral pdb=" CB CYS B 105 " pdb=" SG CYS B 105 " pdb=" SG CYS B 113 " pdb=" CB CYS B 113 " ideal model delta sinusoidal sigma weight residual -86.00 -138.59 52.59 1 1.00e+01 1.00e-02 3.77e+01 dihedral pdb=" CA CYS B 320 " pdb=" C CYS B 320 " pdb=" N CYS B 321 " pdb=" CA CYS B 321 " ideal model delta harmonic sigma weight residual 180.00 159.06 20.94 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 3104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 567 0.036 - 0.072: 252 0.072 - 0.108: 73 0.108 - 0.144: 37 0.144 - 0.180: 2 Chirality restraints: 931 Sorted by residual: chirality pdb=" CA CYS B 321 " pdb=" N CYS B 321 " pdb=" C CYS B 321 " pdb=" CB CYS B 321 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" CA ILE C 163 " pdb=" N ILE C 163 " pdb=" C ILE C 163 " pdb=" CB ILE C 163 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA CYS B 115 " pdb=" N CYS B 115 " pdb=" C CYS B 115 " pdb=" CB CYS B 115 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 928 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 145 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C LYS B 145 " 0.047 2.00e-02 2.50e+03 pdb=" O LYS B 145 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU B 146 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 72 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C GLN B 72 " -0.040 2.00e-02 2.50e+03 pdb=" O GLN B 72 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU B 73 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 267 " 0.038 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO C 268 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 268 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 268 " 0.031 5.00e-02 4.00e+02 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 582 2.74 - 3.28: 5035 3.28 - 3.82: 7526 3.82 - 4.36: 7462 4.36 - 4.90: 13462 Nonbonded interactions: 34067 Sorted by model distance: nonbonded pdb=" O MET A 122 " pdb=" N PHE A 127 " model vdw 2.201 3.120 nonbonded pdb=" O LYS B 292 " pdb=" N ASP B 297 " model vdw 2.208 3.120 nonbonded pdb=" O SER C 96 " pdb=" N SER C 114 " model vdw 2.268 3.120 nonbonded pdb=" O CYS B 320 " pdb=" N THR B 322 " model vdw 2.292 3.120 nonbonded pdb=" O TRP C 491 " pdb=" N ALA C 509 " model vdw 2.342 3.120 ... (remaining 34062 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=0.20 max=1.00 mean=0.95 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: 2.260 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.750 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3443 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 : 0.004 0.069 5134 Z= 0.292 Angle : 0.978 8.505 7138 Z= 0.582 Chirality : 0.047 0.180 931 Planarity : 0.006 0.057 1040 Dihedral : 7.618 54.388 1182 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 1.81 % Allowed : 9.66 % Favored : 88.53 % Rotamer: Outliers : 6.90 % Allowed : 8.05 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.23), residues: 994 helix: -1.41 (0.35), residues: 170 sheet: -1.53 (0.30), residues: 238 loop : -2.51 (0.22), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 73 PHE 0.000 0.000 PHE A 57 TYR 0.000 0.000 TYR A 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 36 average time/residue: 0.0595 time to fit residues: 4.6982 Evaluate side-chains 28 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 328 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.2980 chunk 75 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 40 optimal weight: 0.0570 chunk 77 optimal weight: 10.0000 chunk 30 optimal weight: 0.0570 chunk 47 optimal weight: 10.0000 chunk 57 optimal weight: 0.0670 chunk 89 optimal weight: 4.9990 overall best weight: 0.6956 ------------------------------------------------------------------------------- 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: 0.3543 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5134 Z= 0.234 Angle : 0.666 7.626 7138 Z= 0.371 Chirality : 0.045 0.165 931 Planarity : 0.005 0.055 1040 Dihedral : 6.153 56.242 1016 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.94 % Favored : 93.66 % Rotamer: Outliers : 2.30 % Allowed : 14.94 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.25), residues: 994 helix: 0.63 (0.41), residues: 173 sheet: -1.30 (0.29), residues: 253 loop : -2.13 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 73 PHE 0.000 0.000 PHE A 57 TYR 0.000 0.000 TYR A 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.538 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 26 average time/residue: 0.0505 time to fit residues: 3.2215 Evaluate side-chains 25 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain C residue 599 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 72 optimal weight: 0.0000 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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: 0.3663 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5134 Z= 0.196 Angle : 0.600 5.784 7138 Z= 0.333 Chirality : 0.045 0.138 931 Planarity : 0.005 0.066 1040 Dihedral : 5.553 55.392 1014 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.35 % Favored : 91.45 % Rotamer: Outliers : 3.45 % Allowed : 9.20 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.25), residues: 994 helix: 1.15 (0.41), residues: 175 sheet: -0.83 (0.32), residues: 237 loop : -2.02 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 73 PHE 0.000 0.000 PHE A 57 TYR 0.000 0.000 TYR A 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: B 320 CYS cc_start: 0.0204 (OUTLIER) cc_final: -0.0288 (p) outliers start: 3 outliers final: 1 residues processed: 27 average time/residue: 0.0458 time to fit residues: 2.9653 Evaluate side-chains 25 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 328 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 9.9990 chunk 67 optimal weight: 0.1980 chunk 46 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- 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: 0.4067 moved from start: 0.6548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 5134 Z= 0.497 Angle : 1.035 8.014 7138 Z= 0.611 Chirality : 0.051 0.172 931 Planarity : 0.009 0.073 1040 Dihedral : 9.153 55.386 1014 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.60 % Allowed : 14.08 % Favored : 85.31 % Rotamer: Outliers : 3.45 % Allowed : 10.34 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.36 (0.23), residues: 994 helix: -1.14 (0.35), residues: 167 sheet: -1.23 (0.36), residues: 184 loop : -3.04 (0.21), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 73 PHE 0.000 0.000 PHE A 57 TYR 0.000 0.000 TYR A 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.616 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 26 average time/residue: 0.0734 time to fit residues: 4.5405 Evaluate side-chains 24 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 71 optimal weight: 0.0010 chunk 39 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.5190 ------------------------------------------------------------------------------- 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: 0.3980 moved from start: 0.6635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5134 Z= 0.260 Angle : 0.715 6.952 7138 Z= 0.411 Chirality : 0.046 0.158 931 Planarity : 0.006 0.068 1040 Dihedral : 7.263 58.596 1014 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.97 % Favored : 88.83 % Rotamer: Outliers : 2.30 % Allowed : 11.49 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.24), residues: 994 helix: -0.79 (0.36), residues: 183 sheet: -1.48 (0.34), residues: 218 loop : -3.13 (0.22), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 73 PHE 0.000 0.000 PHE A 57 TYR 0.000 0.000 TYR A 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.525 Fit side-chains REVERT: B 320 CYS cc_start: 0.0404 (OUTLIER) cc_final: 0.0116 (p) outliers start: 2 outliers final: 1 residues processed: 25 average time/residue: 0.0476 time to fit residues: 2.9169 Evaluate side-chains 25 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 328 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 95 optimal weight: 0.4980 chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 chunk 31 optimal weight: 0.0000 chunk 50 optimal weight: 9.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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: 0.3968 moved from start: 0.7283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5134 Z= 0.242 Angle : 0.639 6.043 7138 Z= 0.364 Chirality : 0.045 0.130 931 Planarity : 0.006 0.065 1040 Dihedral : 6.421 56.974 1014 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.18 % Favored : 86.62 % Rotamer: Outliers : 3.45 % Allowed : 11.49 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.24), residues: 994 helix: -0.39 (0.37), residues: 194 sheet: -1.35 (0.34), residues: 213 loop : -3.09 (0.22), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 73 PHE 0.000 0.000 PHE A 57 TYR 0.000 0.000 TYR A 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.490 Fit side-chains REVERT: B 320 CYS cc_start: 0.0235 (OUTLIER) cc_final: -0.0005 (p) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 0.0501 time to fit residues: 3.2674 Evaluate side-chains 27 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 328 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 chunk 69 optimal weight: 0.0370 chunk 80 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 overall best weight: 0.4058 ------------------------------------------------------------------------------- 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: 0.3889 moved from start: 0.7241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 5134 Z= 0.163 Angle : 0.545 5.325 7138 Z= 0.300 Chirality : 0.044 0.127 931 Planarity : 0.005 0.055 1040 Dihedral : 5.609 58.136 1014 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.25 % Favored : 91.55 % Rotamer: Outliers : 4.60 % Allowed : 11.49 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.25), residues: 994 helix: 0.33 (0.39), residues: 194 sheet: -1.41 (0.33), residues: 237 loop : -2.86 (0.23), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 73 PHE 0.000 0.000 PHE A 57 TYR 0.000 0.000 TYR A 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 24 time to evaluate : 0.414 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 28 average time/residue: 0.0484 time to fit residues: 3.1648 Evaluate side-chains 26 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain C residue 323 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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: 0.4072 moved from start: 0.8273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 5134 Z= 0.392 Angle : 0.819 10.592 7138 Z= 0.475 Chirality : 0.047 0.137 931 Planarity : 0.007 0.068 1040 Dihedral : 7.583 58.662 1014 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.70 % Allowed : 16.20 % Favored : 83.10 % Rotamer: Outliers : 4.60 % Allowed : 10.34 % Favored : 85.06 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.47 (0.24), residues: 994 helix: -0.88 (0.35), residues: 194 sheet: -1.88 (0.34), residues: 190 loop : -3.11 (0.22), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 73 PHE 0.000 0.000 PHE A 57 TYR 0.000 0.000 TYR A 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 22 time to evaluate : 0.533 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 26 average time/residue: 0.0504 time to fit residues: 3.1402 Evaluate side-chains 25 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain C residue 323 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.3968 moved from start: 0.8188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 5134 Z= 0.219 Angle : 0.642 12.878 7138 Z= 0.357 Chirality : 0.045 0.182 931 Planarity : 0.006 0.068 1040 Dihedral : 6.470 55.447 1014 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.47 % Favored : 88.23 % Rotamer: Outliers : 3.45 % Allowed : 10.34 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.20 (0.24), residues: 994 helix: -0.36 (0.37), residues: 194 sheet: -1.82 (0.33), residues: 204 loop : -3.00 (0.22), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 73 PHE 0.000 0.000 PHE A 57 TYR 0.000 0.000 TYR A 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.557 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 0.0529 time to fit residues: 3.2527 Evaluate side-chains 25 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain C residue 323 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 10.0000 chunk 65 optimal weight: 0.0970 chunk 98 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 78 optimal weight: 0.0470 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 overall best weight: 0.4276 ------------------------------------------------------------------------------- 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: 0.3907 moved from start: 0.8164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 5134 Z= 0.181 Angle : 0.555 6.463 7138 Z= 0.304 Chirality : 0.044 0.127 931 Planarity : 0.005 0.056 1040 Dihedral : 5.552 53.457 1014 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.87 % Favored : 88.83 % Rotamer: Outliers : 3.45 % Allowed : 10.34 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.76 (0.26), residues: 994 helix: 0.38 (0.39), residues: 200 sheet: -1.62 (0.33), residues: 217 loop : -2.88 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 73 PHE 0.000 0.000 PHE A 57 TYR 0.000 0.000 TYR A 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 27 average time/residue: 0.0523 time to fit residues: 3.4070 Evaluate side-chains 26 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain C residue 323 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 30.0000 chunk 78 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 9 optimal weight: 0.2980 chunk 14 optimal weight: 0.0670 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.209678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.194732 restraints weight = 17724.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.195458 restraints weight = 15816.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.196485 restraints weight = 13305.868| |-----------------------------------------------------------------------------| r_work (final): 0.4632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4632 r_free = 0.4632 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4616 r_free = 0.4616 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 150 | |-----------------------------------------------------------------------------| r_final: 0.4616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4136 moved from start: 0.8286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 5134 Z= 0.210 Angle : 0.630 19.843 7138 Z= 0.340 Chirality : 0.044 0.163 931 Planarity : 0.005 0.054 1040 Dihedral : 5.683 50.849 1014 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.07 % Favored : 88.63 % Rotamer: Outliers : 3.45 % Allowed : 11.49 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.69 (0.26), residues: 994 helix: 0.49 (0.40), residues: 200 sheet: -1.75 (0.33), residues: 230 loop : -2.79 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 73 PHE 0.000 0.000 PHE A 57 TYR 0.000 0.000 TYR A 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1278.80 seconds wall clock time: 23 minutes 32.57 seconds (1412.57 seconds total)