Starting phenix.real_space_refine on Mon Mar 11 02:39:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf8_25077/03_2024/7sf8_25077_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf8_25077/03_2024/7sf8_25077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf8_25077/03_2024/7sf8_25077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf8_25077/03_2024/7sf8_25077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf8_25077/03_2024/7sf8_25077_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf8_25077/03_2024/7sf8_25077_neut.pdb" } resolution = 2.7 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= 0.015 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 4266 2.51 5 N 1111 2.21 5 O 1239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 394": "OE1" <-> "OE2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "A ARG 559": "NH1" <-> "NH2" Residue "A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6661 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1993 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 250} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1708 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2582 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 378 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 3.86, per 1000 atoms: 0.58 Number of scatterers: 6661 At special positions: 0 Unit cell: (102.389, 93.7116, 118.007, 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 1239 8.00 N 1111 7.00 C 4266 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 469 " - pdb=" SG CYS A 556 " distance=2.09 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 1.2 seconds 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1624 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 42.3% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.625A pdb=" N VAL A 387 " --> pdb=" O TYR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 427 removed outlier: 3.640A pdb=" N HIS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR A 402 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 464 removed outlier: 3.901A pdb=" N LYS A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 457 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLU A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) Proline residue: A 459 - end of helix removed outlier: 3.580A pdb=" N LEU A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A 463 " --> pdb=" O PRO A 459 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 499 removed outlier: 4.173A pdb=" N ALA A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 474 " --> pdb=" O ARG A 470 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 529 removed outlier: 3.585A pdb=" N MET A 516 " --> pdb=" O LYS A 512 " (cutoff:3.500A) Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 532 through 534 No H-bonds generated for 'chain 'A' and resid 532 through 534' Processing helix chain 'A' and resid 560 through 568 removed outlier: 4.043A pdb=" N SER A 564 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 591 Processing helix chain 'A' and resid 602 through 614 Processing helix chain 'A' and resid 615 through 625 removed outlier: 4.055A pdb=" N PHE A 624 " --> pdb=" O PHE A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 643 removed outlier: 3.518A pdb=" N VAL A 633 " --> pdb=" O PHE A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'B' and resid 12 through 26 removed outlier: 3.579A pdb=" N SER B 16 " --> pdb=" O ALA B 12 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU B 26 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 32 removed outlier: 3.679A pdb=" N VAL B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 117 through 130 removed outlier: 3.607A pdb=" N SER B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 171 through 185 Processing helix chain 'B' and resid 206 through 228 removed outlier: 3.708A pdb=" N ASP B 222 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 10 through 24 removed outlier: 3.540A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 537 Processing sheet with id=AA2, first strand: chain 'B' and resid 69 through 75 removed outlier: 3.552A pdb=" N VAL B 34 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS B 35 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU B 107 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU B 37 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 39 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.755A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 4.057A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.716A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.751A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.787A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.842A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.785A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) 313 hydrogen bonds defined for protein. 891 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: 1.81 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1784 1.33 - 1.46: 1405 1.46 - 1.58: 3538 1.58 - 1.70: 0 1.70 - 1.83: 65 Bond restraints: 6792 Sorted by residual: bond pdb=" CA SER A 465 " pdb=" CB SER A 465 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.43e-02 4.89e+03 2.80e+01 bond pdb=" CA SER A 564 " pdb=" CB SER A 564 " ideal model delta sigma weight residual 1.529 1.463 0.066 1.55e-02 4.16e+03 1.83e+01 bond pdb=" CA SER A 472 " pdb=" CB SER A 472 " ideal model delta sigma weight residual 1.528 1.461 0.067 1.59e-02 3.96e+03 1.78e+01 bond pdb=" CA SER A 561 " pdb=" CB SER A 561 " ideal model delta sigma weight residual 1.531 1.468 0.063 1.56e-02 4.11e+03 1.63e+01 bond pdb=" N ILE A 558 " pdb=" CA ILE A 558 " ideal model delta sigma weight residual 1.458 1.506 -0.048 1.20e-02 6.94e+03 1.57e+01 ... (remaining 6787 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.77: 80 105.77 - 112.84: 3688 112.84 - 119.92: 2296 119.92 - 126.99: 3080 126.99 - 134.07: 72 Bond angle restraints: 9216 Sorted by residual: angle pdb=" N ARG A 470 " pdb=" CA ARG A 470 " pdb=" C ARG A 470 " ideal model delta sigma weight residual 113.50 106.46 7.04 1.23e+00 6.61e-01 3.27e+01 angle pdb=" N GLN B 226 " pdb=" CA GLN B 226 " pdb=" C GLN B 226 " ideal model delta sigma weight residual 113.12 106.97 6.15 1.25e+00 6.40e-01 2.42e+01 angle pdb=" N LEU A 481 " pdb=" CA LEU A 481 " pdb=" C LEU A 481 " ideal model delta sigma weight residual 113.18 107.56 5.62 1.21e+00 6.83e-01 2.16e+01 angle pdb=" N ALA A 467 " pdb=" CA ALA A 467 " pdb=" CB ALA A 467 " ideal model delta sigma weight residual 110.59 105.33 5.26 1.33e+00 5.65e-01 1.57e+01 angle pdb=" N MET A 655 " pdb=" CA MET A 655 " pdb=" C MET A 655 " ideal model delta sigma weight residual 111.36 107.22 4.14 1.09e+00 8.42e-01 1.44e+01 ... (remaining 9211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 3644 17.21 - 34.43: 307 34.43 - 51.64: 51 51.64 - 68.85: 5 68.85 - 86.06: 4 Dihedral angle restraints: 4011 sinusoidal: 1508 harmonic: 2503 Sorted by residual: dihedral pdb=" CA ASP C 258 " pdb=" C ASP C 258 " pdb=" N GLN C 259 " pdb=" CA GLN C 259 " ideal model delta harmonic sigma weight residual 180.00 159.32 20.68 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA VAL A 531 " pdb=" C VAL A 531 " pdb=" N ASP A 532 " pdb=" CA ASP A 532 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ARG A 429 " pdb=" C ARG A 429 " pdb=" N ARG A 430 " pdb=" CA ARG A 430 " ideal model delta harmonic sigma weight residual 180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 4008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 860 0.056 - 0.113: 174 0.113 - 0.169: 38 0.169 - 0.226: 5 0.226 - 0.282: 2 Chirality restraints: 1079 Sorted by residual: chirality pdb=" CA TYR A 536 " pdb=" N TYR A 536 " pdb=" C TYR A 536 " pdb=" CB TYR A 536 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ILE A 540 " pdb=" N ILE A 540 " pdb=" C ILE A 540 " pdb=" CB ILE A 540 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ARG A 470 " pdb=" N ARG A 470 " pdb=" C ARG A 470 " pdb=" CB ARG A 470 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1076 not shown) Planarity restraints: 1160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 469 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.28e+00 pdb=" C CYS A 469 " -0.053 2.00e-02 2.50e+03 pdb=" O CYS A 469 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG A 470 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 558 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.32e+00 pdb=" C ILE A 558 " 0.043 2.00e-02 2.50e+03 pdb=" O ILE A 558 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG A 559 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 557 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.82e+00 pdb=" C TRP A 557 " -0.038 2.00e-02 2.50e+03 pdb=" O TRP A 557 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE A 558 " 0.013 2.00e-02 2.50e+03 ... (remaining 1157 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1607 2.80 - 3.32: 5912 3.32 - 3.85: 10104 3.85 - 4.37: 12052 4.37 - 4.90: 21621 Nonbonded interactions: 51296 Sorted by model distance: nonbonded pdb=" NE1 TRP A 617 " pdb=" OE1 GLN A 644 " model vdw 2.270 2.520 nonbonded pdb=" O TYR A 505 " pdb=" NH2 ARG B 32 " model vdw 2.298 2.520 nonbonded pdb=" O GLY B 40 " pdb=" NH2 ARG B 90 " model vdw 2.371 2.520 nonbonded pdb=" O VAL A 563 " pdb=" OG1 THR A 567 " model vdw 2.387 2.440 nonbonded pdb=" O ASP C 228 " pdb=" OG SER C 245 " model vdw 2.397 2.440 ... (remaining 51291 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 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: 9.430 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.200 Find NCS groups from input model: 0.160 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: 0.000 Load rotamer database and sin/cos tables:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 : 0.005 0.076 6792 Z= 0.347 Angle : 0.740 7.037 9216 Z= 0.475 Chirality : 0.050 0.282 1079 Planarity : 0.004 0.054 1160 Dihedral : 13.034 86.064 2384 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.14 % Allowed : 0.97 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.30), residues: 846 helix: 1.57 (0.30), residues: 341 sheet: 0.81 (0.41), residues: 161 loop : -1.40 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.004 0.001 HIS B 221 PHE 0.021 0.002 PHE A 649 TYR 0.014 0.002 TYR A 408 ARG 0.006 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 0.736 Fit side-chains REVERT: A 506 VAL cc_start: 0.8055 (t) cc_final: 0.7849 (t) REVERT: A 520 PHE cc_start: 0.7693 (t80) cc_final: 0.7443 (t80) REVERT: A 580 MET cc_start: 0.8415 (mmm) cc_final: 0.8156 (mmt) REVERT: A 590 ILE cc_start: 0.8046 (mm) cc_final: 0.7796 (mp) REVERT: B 89 GLN cc_start: 0.6281 (mp-120) cc_final: 0.6060 (mp-120) REVERT: B 147 ASP cc_start: 0.7144 (p0) cc_final: 0.6789 (p0) REVERT: B 151 GLU cc_start: 0.7436 (mp0) cc_final: 0.6841 (mp0) outliers start: 1 outliers final: 1 residues processed: 141 average time/residue: 1.3489 time to fit residues: 198.7592 Evaluate side-chains 120 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 34 optimal weight: 0.2980 chunk 65 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 0.0770 chunk 76 optimal weight: 3.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 268 ASN C 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6792 Z= 0.204 Angle : 0.510 5.419 9216 Z= 0.275 Chirality : 0.042 0.146 1079 Planarity : 0.004 0.052 1160 Dihedral : 4.408 48.998 919 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.81 % Allowed : 9.74 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.30), residues: 846 helix: 1.96 (0.31), residues: 348 sheet: 1.09 (0.41), residues: 171 loop : -1.28 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 486 HIS 0.005 0.001 HIS A 401 PHE 0.020 0.001 PHE A 649 TYR 0.011 0.001 TYR A 408 ARG 0.004 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 0.696 Fit side-chains REVERT: A 555 MET cc_start: 0.7131 (tmm) cc_final: 0.6832 (ttp) REVERT: A 580 MET cc_start: 0.8339 (mmm) cc_final: 0.8073 (mmt) REVERT: A 590 ILE cc_start: 0.8059 (mm) cc_final: 0.7822 (mp) REVERT: B 20 ASP cc_start: 0.8176 (m-30) cc_final: 0.7789 (m-30) REVERT: B 89 GLN cc_start: 0.6291 (mp-120) cc_final: 0.6088 (mp-120) REVERT: B 147 ASP cc_start: 0.7212 (p0) cc_final: 0.6987 (p0) REVERT: B 151 GLU cc_start: 0.7433 (mp0) cc_final: 0.6924 (mp0) REVERT: C 164 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8334 (m) outliers start: 13 outliers final: 3 residues processed: 134 average time/residue: 1.1314 time to fit residues: 159.8741 Evaluate side-chains 120 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 228 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 51 optimal weight: 0.0050 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 61 optimal weight: 0.2980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 268 ASN C 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6792 Z= 0.237 Angle : 0.504 6.012 9216 Z= 0.273 Chirality : 0.042 0.136 1079 Planarity : 0.004 0.051 1160 Dihedral : 4.069 17.280 915 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.67 % Allowed : 13.07 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.30), residues: 846 helix: 2.03 (0.30), residues: 349 sheet: 1.03 (0.41), residues: 173 loop : -1.27 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 82 HIS 0.005 0.001 HIS B 221 PHE 0.024 0.002 PHE A 629 TYR 0.011 0.001 TYR A 408 ARG 0.007 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 0.724 Fit side-chains REVERT: A 555 MET cc_start: 0.6956 (tmm) cc_final: 0.6637 (ttt) REVERT: A 580 MET cc_start: 0.8251 (mmm) cc_final: 0.7994 (mmt) REVERT: B 20 ASP cc_start: 0.8156 (m-30) cc_final: 0.7745 (m-30) REVERT: B 89 GLN cc_start: 0.6401 (mp-120) cc_final: 0.6141 (mp-120) REVERT: C 164 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8351 (m) outliers start: 12 outliers final: 6 residues processed: 128 average time/residue: 1.2671 time to fit residues: 170.7746 Evaluate side-chains 118 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain C residue 164 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN C 268 ASN C 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6792 Z= 0.345 Angle : 0.574 7.791 9216 Z= 0.304 Chirality : 0.045 0.146 1079 Planarity : 0.004 0.054 1160 Dihedral : 4.265 16.878 915 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.50 % Allowed : 13.91 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.30), residues: 846 helix: 1.94 (0.30), residues: 349 sheet: 0.99 (0.40), residues: 171 loop : -1.30 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.006 0.001 HIS A 401 PHE 0.028 0.002 PHE A 649 TYR 0.011 0.002 TYR A 384 ARG 0.007 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 0.756 Fit side-chains REVERT: A 555 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.6662 (ttt) REVERT: A 580 MET cc_start: 0.8232 (mmm) cc_final: 0.8014 (mmt) REVERT: B 89 GLN cc_start: 0.6430 (mp-120) cc_final: 0.6191 (mp-120) REVERT: B 147 ASP cc_start: 0.7575 (p0) cc_final: 0.7281 (p0) REVERT: B 151 GLU cc_start: 0.7478 (mp0) cc_final: 0.7007 (mp0) REVERT: B 181 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7039 (mm-30) REVERT: B 209 ARG cc_start: 0.6306 (OUTLIER) cc_final: 0.5978 (mtm110) REVERT: C 20 ASP cc_start: 0.7257 (m-30) cc_final: 0.7019 (m-30) REVERT: C 164 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8478 (m) outliers start: 18 outliers final: 10 residues processed: 118 average time/residue: 1.2978 time to fit residues: 160.5417 Evaluate side-chains 121 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 228 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 0.0470 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 0 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN C 268 ASN C 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6792 Z= 0.225 Angle : 0.501 6.500 9216 Z= 0.267 Chirality : 0.042 0.132 1079 Planarity : 0.003 0.051 1160 Dihedral : 4.079 23.121 915 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.78 % Allowed : 14.74 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.30), residues: 846 helix: 2.17 (0.30), residues: 350 sheet: 0.92 (0.40), residues: 173 loop : -1.21 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS A 401 PHE 0.023 0.001 PHE A 649 TYR 0.010 0.001 TYR A 408 ARG 0.007 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 495 TYR cc_start: 0.8214 (t80) cc_final: 0.7981 (t80) REVERT: A 555 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6628 (ttt) REVERT: A 580 MET cc_start: 0.8223 (mmm) cc_final: 0.8000 (mmt) REVERT: B 89 GLN cc_start: 0.6411 (mp-120) cc_final: 0.6169 (mp-120) REVERT: B 147 ASP cc_start: 0.7555 (p0) cc_final: 0.7317 (p0) REVERT: B 151 GLU cc_start: 0.7459 (mp0) cc_final: 0.7028 (mp0) REVERT: B 181 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7065 (mm-30) REVERT: C 20 ASP cc_start: 0.7256 (m-30) cc_final: 0.7010 (m-30) REVERT: C 164 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8395 (m) outliers start: 20 outliers final: 14 residues processed: 121 average time/residue: 1.3355 time to fit residues: 169.5913 Evaluate side-chains 126 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 228 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.0570 chunk 73 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 42 optimal weight: 0.0170 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN C 175 GLN C 259 GLN C 268 ASN C 293 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6792 Z= 0.174 Angle : 0.474 6.268 9216 Z= 0.253 Chirality : 0.041 0.135 1079 Planarity : 0.003 0.048 1160 Dihedral : 3.903 25.337 915 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.06 % Allowed : 15.44 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.09 (0.30), residues: 846 helix: 2.32 (0.30), residues: 351 sheet: 0.95 (0.42), residues: 168 loop : -1.26 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS A 401 PHE 0.021 0.001 PHE A 649 TYR 0.009 0.001 TYR A 408 ARG 0.005 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 495 TYR cc_start: 0.8179 (t80) cc_final: 0.7957 (t80) REVERT: A 555 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6516 (ttt) REVERT: A 580 MET cc_start: 0.8203 (mmm) cc_final: 0.7992 (mmt) REVERT: B 20 ASP cc_start: 0.8119 (m-30) cc_final: 0.7720 (m-30) REVERT: B 89 GLN cc_start: 0.6408 (mp-120) cc_final: 0.6125 (mp-120) REVERT: B 151 GLU cc_start: 0.7428 (mp0) cc_final: 0.7027 (mp0) REVERT: B 181 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7055 (mm-30) REVERT: C 20 ASP cc_start: 0.7272 (m-30) cc_final: 0.7028 (m-30) REVERT: C 164 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8327 (m) outliers start: 22 outliers final: 15 residues processed: 131 average time/residue: 1.2595 time to fit residues: 172.9189 Evaluate side-chains 132 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 228 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN C 268 ASN C 293 ASN C 340 ASN D 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 6792 Z= 0.387 Angle : 0.579 7.761 9216 Z= 0.307 Chirality : 0.046 0.152 1079 Planarity : 0.004 0.052 1160 Dihedral : 4.210 18.179 915 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.34 % Allowed : 15.58 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.30), residues: 846 helix: 2.26 (0.30), residues: 340 sheet: 0.85 (0.41), residues: 168 loop : -1.26 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.005 0.001 HIS A 401 PHE 0.028 0.002 PHE A 649 TYR 0.016 0.002 TYR A 402 ARG 0.006 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 0.800 Fit side-chains REVERT: A 555 MET cc_start: 0.6896 (OUTLIER) cc_final: 0.6639 (ttt) REVERT: B 89 GLN cc_start: 0.6432 (mp-120) cc_final: 0.6048 (mp-120) REVERT: B 98 GLU cc_start: 0.5820 (OUTLIER) cc_final: 0.3326 (mm-30) REVERT: B 147 ASP cc_start: 0.7697 (p0) cc_final: 0.7435 (p0) REVERT: B 151 GLU cc_start: 0.7495 (mp0) cc_final: 0.7060 (mp0) REVERT: B 181 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7046 (mm-30) REVERT: C 20 ASP cc_start: 0.7287 (m-30) cc_final: 0.7008 (m-30) REVERT: C 44 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7711 (mt0) REVERT: C 164 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8531 (m) outliers start: 24 outliers final: 15 residues processed: 114 average time/residue: 1.4160 time to fit residues: 168.8528 Evaluate side-chains 122 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 228 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN C 268 ASN C 293 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6792 Z= 0.249 Angle : 0.513 6.261 9216 Z= 0.274 Chirality : 0.042 0.135 1079 Planarity : 0.003 0.050 1160 Dihedral : 4.005 17.657 915 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.20 % Allowed : 15.86 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.06 (0.30), residues: 846 helix: 2.41 (0.30), residues: 340 sheet: 0.82 (0.40), residues: 173 loop : -1.23 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 82 HIS 0.004 0.001 HIS A 401 PHE 0.024 0.001 PHE A 649 TYR 0.011 0.001 TYR A 408 ARG 0.005 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 0.726 Fit side-chains REVERT: A 555 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6526 (ttt) REVERT: B 89 GLN cc_start: 0.6398 (mp-120) cc_final: 0.6145 (mp-120) REVERT: B 151 GLU cc_start: 0.7465 (mp0) cc_final: 0.7031 (mp0) REVERT: B 181 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7065 (mm-30) REVERT: C 164 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8446 (m) outliers start: 23 outliers final: 18 residues processed: 122 average time/residue: 1.2751 time to fit residues: 163.2891 Evaluate side-chains 126 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 336 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 68 optimal weight: 2.9990 chunk 71 optimal weight: 0.0980 chunk 49 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN C 268 ASN C 293 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6792 Z= 0.237 Angle : 0.518 6.969 9216 Z= 0.276 Chirality : 0.042 0.135 1079 Planarity : 0.004 0.049 1160 Dihedral : 3.958 20.017 915 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.06 % Allowed : 16.41 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.30), residues: 846 helix: 2.33 (0.30), residues: 348 sheet: 0.84 (0.41), residues: 173 loop : -1.29 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS A 401 PHE 0.023 0.001 PHE A 649 TYR 0.023 0.001 TYR A 495 ARG 0.007 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 0.750 Fit side-chains REVERT: A 555 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.6615 (ttt) REVERT: B 89 GLN cc_start: 0.6435 (mp-120) cc_final: 0.6145 (mp-120) REVERT: B 151 GLU cc_start: 0.7464 (mp0) cc_final: 0.7040 (mp0) REVERT: B 181 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7072 (mm-30) REVERT: C 164 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8407 (m) outliers start: 22 outliers final: 17 residues processed: 120 average time/residue: 1.2812 time to fit residues: 161.2331 Evaluate side-chains 126 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 83 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 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 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN C 268 ASN C 293 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6792 Z= 0.275 Angle : 0.539 6.498 9216 Z= 0.287 Chirality : 0.043 0.146 1079 Planarity : 0.004 0.050 1160 Dihedral : 4.038 19.954 915 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.06 % Allowed : 16.69 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.30), residues: 846 helix: 2.30 (0.30), residues: 347 sheet: 0.82 (0.40), residues: 173 loop : -1.31 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 82 HIS 0.004 0.001 HIS B 221 PHE 0.024 0.002 PHE A 649 TYR 0.010 0.001 TYR A 408 ARG 0.008 0.000 ARG B 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 105 time to evaluate : 0.667 Fit side-chains REVERT: A 555 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6621 (ttt) REVERT: B 89 GLN cc_start: 0.6435 (mp-120) cc_final: 0.6147 (mp-120) REVERT: B 151 GLU cc_start: 0.7476 (mp0) cc_final: 0.7040 (mp0) REVERT: B 181 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7071 (mm-30) REVERT: C 164 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8464 (m) outliers start: 22 outliers final: 17 residues processed: 118 average time/residue: 1.2887 time to fit residues: 159.5574 Evaluate side-chains 125 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.0970 chunk 58 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN C 268 ASN C 293 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.127062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.107792 restraints weight = 9606.540| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.84 r_work: 0.3362 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6792 Z= 0.243 Angle : 0.520 6.221 9216 Z= 0.277 Chirality : 0.043 0.141 1079 Planarity : 0.004 0.049 1160 Dihedral : 3.956 19.880 915 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.64 % Allowed : 17.25 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.30), residues: 846 helix: 2.34 (0.30), residues: 348 sheet: 0.86 (0.40), residues: 173 loop : -1.32 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 82 HIS 0.003 0.001 HIS A 401 PHE 0.024 0.001 PHE A 649 TYR 0.010 0.001 TYR A 408 ARG 0.008 0.000 ARG B 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3276.84 seconds wall clock time: 58 minutes 59.09 seconds (3539.09 seconds total)