Starting phenix.real_space_refine on Thu Dec 7 19:44:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnb_34909/12_2023/8hnb_34909.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnb_34909/12_2023/8hnb_34909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnb_34909/12_2023/8hnb_34909.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnb_34909/12_2023/8hnb_34909.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnb_34909/12_2023/8hnb_34909.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnb_34909/12_2023/8hnb_34909.pdb" } resolution = 3.53 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= 0.021 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 32 5.16 5 C 2689 2.51 5 N 649 2.21 5 O 713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 58": "NH1" <-> "NH2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 197": "OD1" <-> "OD2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4083 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4041 Classifications: {'peptide': 562} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 19, 'TRANS': 542} Chain breaks: 3 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 438 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 10, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 189 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.74, per 1000 atoms: 0.67 Number of scatterers: 4083 At special positions: 0 Unit cell: (101.504, 59.072, 79.872, 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 32 16.00 O 713 8.00 N 649 7.00 C 2689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.02 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.04 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.04 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " distance=2.02 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 701 " - " ASN A 516 " " NAG B 1 " - " ASN A 503 " Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 799.5 milliseconds 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 69.2% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 26 through 60 removed outlier: 4.140A pdb=" N PHE A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N HIS A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A 58 " --> pdb=" O HIS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 91 removed outlier: 3.900A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS A 90 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 removed outlier: 3.794A pdb=" N LEU A 96 " --> pdb=" O HIS A 92 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY A 98 " --> pdb=" O PRO A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.588A pdb=" N MET A 118 " --> pdb=" O HIS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.546A pdb=" N LYS A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 removed outlier: 3.596A pdb=" N VAL A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 180 " --> pdb=" O MET A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 199 Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.971A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.782A pdb=" N ILE A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 Processing helix chain 'A' and resid 257 through 273 removed outlier: 3.516A pdb=" N SER A 265 " --> pdb=" O ASN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 279 removed outlier: 3.923A pdb=" N PHE A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 335 through 366 removed outlier: 5.212A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 401 removed outlier: 3.846A pdb=" N ILE A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 403 through 428 removed outlier: 3.571A pdb=" N PHE A 421 " --> pdb=" O MET A 417 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 426 " --> pdb=" O TYR A 422 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 removed outlier: 4.131A pdb=" N ASP A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 550 removed outlier: 3.515A pdb=" N THR A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 563 removed outlier: 3.710A pdb=" N HIS A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 559 " --> pdb=" O HIS A 555 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 560 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 582 removed outlier: 3.597A pdb=" N LEU A 582 " --> pdb=" O VAL A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 598 removed outlier: 4.442A pdb=" N ILE A 589 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 593 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 651 Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436 removed outlier: 6.594A pdb=" N PHE A 501 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N SER A 492 " --> pdb=" O PHE A 501 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN A 503 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 599 through 602 removed outlier: 7.059A pdb=" N THR A 615 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP A 602 " --> pdb=" O CYS A 613 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N CYS A 613 " --> pdb=" O TRP A 602 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 768 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: 1.11 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 744 1.33 - 1.45: 1084 1.45 - 1.57: 2302 1.57 - 1.69: 0 1.69 - 1.82: 48 Bond restraints: 4178 Sorted by residual: bond pdb=" C4 NAG B 1 " pdb=" O4 NAG B 1 " ideal model delta sigma weight residual 1.409 1.481 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" CA ALA A 581 " pdb=" C ALA A 581 " ideal model delta sigma weight residual 1.524 1.484 0.039 1.26e-02 6.30e+03 9.75e+00 bond pdb=" CA ILE A 428 " pdb=" C ILE A 428 " ideal model delta sigma weight residual 1.520 1.557 -0.037 1.26e-02 6.30e+03 8.62e+00 bond pdb=" C GLN A 369 " pdb=" N PRO A 370 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.08e-02 8.57e+03 8.23e+00 bond pdb=" C TYR A 640 " pdb=" O TYR A 640 " ideal model delta sigma weight residual 1.236 1.205 0.032 1.15e-02 7.56e+03 7.57e+00 ... (remaining 4173 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.14: 76 105.14 - 112.37: 2003 112.37 - 119.60: 1404 119.60 - 126.83: 2152 126.83 - 134.06: 41 Bond angle restraints: 5676 Sorted by residual: angle pdb=" N TYR A 121 " pdb=" CA TYR A 121 " pdb=" C TYR A 121 " ideal model delta sigma weight residual 109.15 98.24 10.91 1.44e+00 4.82e-01 5.74e+01 angle pdb=" N PHE A 591 " pdb=" CA PHE A 591 " pdb=" C PHE A 591 " ideal model delta sigma weight residual 111.14 104.03 7.11 1.08e+00 8.57e-01 4.33e+01 angle pdb=" N GLU A 364 " pdb=" CA GLU A 364 " pdb=" C GLU A 364 " ideal model delta sigma weight residual 111.36 118.51 -7.15 1.09e+00 8.42e-01 4.30e+01 angle pdb=" N LEU A 113 " pdb=" CA LEU A 113 " pdb=" C LEU A 113 " ideal model delta sigma weight residual 109.81 123.05 -13.24 2.21e+00 2.05e-01 3.59e+01 angle pdb=" N TYR A 502 " pdb=" CA TYR A 502 " pdb=" C TYR A 502 " ideal model delta sigma weight residual 110.42 119.66 -9.24 1.55e+00 4.16e-01 3.55e+01 ... (remaining 5671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.06: 2303 21.06 - 42.12: 133 42.12 - 63.18: 16 63.18 - 84.24: 2 84.24 - 105.30: 8 Dihedral angle restraints: 2462 sinusoidal: 861 harmonic: 1601 Sorted by residual: dihedral pdb=" CB CYS A 430 " pdb=" SG CYS A 430 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual -86.00 -129.16 43.16 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" N ILE A 407 " pdb=" C ILE A 407 " pdb=" CA ILE A 407 " pdb=" CB ILE A 407 " ideal model delta harmonic sigma weight residual 123.40 135.31 -11.91 0 2.50e+00 1.60e-01 2.27e+01 dihedral pdb=" C ILE A 407 " pdb=" N ILE A 407 " pdb=" CA ILE A 407 " pdb=" CB ILE A 407 " ideal model delta harmonic sigma weight residual -122.00 -133.65 11.65 0 2.50e+00 1.60e-01 2.17e+01 ... (remaining 2459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 523 0.083 - 0.166: 114 0.166 - 0.249: 23 0.249 - 0.332: 8 0.332 - 0.415: 5 Chirality restraints: 673 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.67e+02 chirality pdb=" CA LEU A 113 " pdb=" N LEU A 113 " pdb=" C LEU A 113 " pdb=" CB LEU A 113 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CA SER A 140 " pdb=" N SER A 140 " pdb=" C SER A 140 " pdb=" CB SER A 140 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 ... (remaining 670 not shown) Planarity restraints: 700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.310 2.00e-02 2.50e+03 2.61e-01 8.49e+02 pdb=" C7 NAG B 2 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.448 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 701 " -0.290 2.00e-02 2.50e+03 2.44e-01 7.42e+02 pdb=" C7 NAG A 701 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A 701 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG A 701 " 0.415 2.00e-02 2.50e+03 pdb=" O7 NAG A 701 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.140 2.00e-02 2.50e+03 1.18e-01 1.75e+02 pdb=" C7 NAG B 1 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.189 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.113 2.00e-02 2.50e+03 ... (remaining 697 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 1748 2.89 - 3.39: 4409 3.39 - 3.89: 6500 3.89 - 4.40: 7456 4.40 - 4.90: 12134 Nonbonded interactions: 32247 Sorted by model distance: nonbonded pdb=" O SER A 140 " pdb=" N CYS A 485 " model vdw 2.382 2.520 nonbonded pdb=" O3 NAG B 1 " pdb=" O5 NAG B 2 " model vdw 2.455 2.440 nonbonded pdb=" OG SER A 328 " pdb=" CD2 LEU A 570 " model vdw 2.458 3.460 nonbonded pdb=" N GLY A 223 " pdb=" N PHE A 224 " model vdw 2.460 2.560 nonbonded pdb=" N SER A 457 " pdb=" O SER A 457 " model vdw 2.496 2.496 ... (remaining 32242 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 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: 0.910 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: 3.680 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.030 Find NCS groups from input model: 0.110 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 4178 Z= 0.446 Angle : 1.349 13.238 5676 Z= 0.919 Chirality : 0.083 0.415 673 Planarity : 0.016 0.261 698 Dihedral : 14.650 105.302 1421 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.09 % Allowed : 9.92 % Favored : 87.99 % Cbeta Deviations : 0.39 % 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: -0.66 (0.33), residues: 554 helix: 0.20 (0.27), residues: 342 sheet: None (None), residues: 0 loop : -1.42 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 259 HIS 0.003 0.001 HIS A 575 PHE 0.014 0.001 PHE A 574 TYR 0.025 0.002 TYR A 338 ARG 0.002 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 0.396 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 125 average time/residue: 0.1807 time to fit residues: 27.3264 Evaluate side-chains 86 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.0570 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 366 GLN A 541 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4178 Z= 0.249 Angle : 0.736 10.434 5676 Z= 0.355 Chirality : 0.044 0.267 673 Planarity : 0.004 0.029 698 Dihedral : 8.276 58.246 654 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.13 % Allowed : 17.23 % Favored : 79.63 % 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: 0.39 (0.34), residues: 554 helix: 1.21 (0.27), residues: 340 sheet: -5.39 (0.52), residues: 5 loop : -1.15 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 171 HIS 0.005 0.001 HIS A 204 PHE 0.013 0.001 PHE A 73 TYR 0.021 0.002 TYR A 338 ARG 0.008 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 104 average time/residue: 0.1790 time to fit residues: 22.7741 Evaluate side-chains 86 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.445 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0443 time to fit residues: 1.1627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 55 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 40 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4178 Z= 0.219 Angle : 0.674 10.087 5676 Z= 0.325 Chirality : 0.040 0.225 673 Planarity : 0.003 0.034 698 Dihedral : 6.082 57.816 654 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.44 % Allowed : 18.54 % Favored : 77.02 % 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: 1.11 (0.35), residues: 554 helix: 1.58 (0.27), residues: 344 sheet: None (None), residues: 0 loop : -0.65 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 602 HIS 0.016 0.003 HIS A 115 PHE 0.011 0.001 PHE A 73 TYR 0.040 0.002 TYR A 590 ARG 0.008 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.439 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 104 average time/residue: 0.1997 time to fit residues: 25.0457 Evaluate side-chains 94 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.592 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0428 time to fit residues: 1.2472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7323 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4178 Z= 0.243 Angle : 0.652 9.435 5676 Z= 0.317 Chirality : 0.041 0.219 673 Planarity : 0.004 0.035 698 Dihedral : 5.520 55.811 654 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.61 % Allowed : 19.06 % Favored : 78.33 % 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: 1.17 (0.35), residues: 554 helix: 1.65 (0.27), residues: 342 sheet: None (None), residues: 0 loop : -0.65 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.004 0.001 HIS A 115 PHE 0.013 0.001 PHE A 73 TYR 0.042 0.002 TYR A 590 ARG 0.007 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.467 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 93 average time/residue: 0.1991 time to fit residues: 22.2994 Evaluate side-chains 87 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.473 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0437 time to fit residues: 0.8541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.0030 chunk 22 optimal weight: 0.0050 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 30.0000 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4178 Z= 0.193 Angle : 0.647 9.426 5676 Z= 0.309 Chirality : 0.040 0.203 673 Planarity : 0.004 0.041 698 Dihedral : 5.387 55.834 654 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.78 % Allowed : 20.89 % Favored : 78.33 % 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: 1.28 (0.35), residues: 554 helix: 1.83 (0.27), residues: 341 sheet: None (None), residues: 0 loop : -0.78 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.003 0.001 HIS A 575 PHE 0.013 0.001 PHE A 73 TYR 0.038 0.002 TYR A 590 ARG 0.011 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.355 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 90 average time/residue: 0.2002 time to fit residues: 21.6872 Evaluate side-chains 85 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.458 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0531 time to fit residues: 0.9022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.0040 chunk 28 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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: 0.7323 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4178 Z= 0.216 Angle : 0.662 9.449 5676 Z= 0.314 Chirality : 0.040 0.194 673 Planarity : 0.004 0.049 698 Dihedral : 5.286 55.718 654 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.04 % Allowed : 21.15 % Favored : 77.81 % 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: 1.24 (0.35), residues: 554 helix: 1.69 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -0.68 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 470 HIS 0.002 0.001 HIS A 115 PHE 0.015 0.001 PHE A 391 TYR 0.037 0.001 TYR A 590 ARG 0.011 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.450 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 89 average time/residue: 0.1991 time to fit residues: 21.4561 Evaluate side-chains 85 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.463 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0425 time to fit residues: 0.7010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 50.0000 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7351 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4178 Z= 0.247 Angle : 0.673 9.432 5676 Z= 0.320 Chirality : 0.041 0.187 673 Planarity : 0.004 0.051 698 Dihedral : 5.333 55.890 654 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.61 % Allowed : 21.93 % Favored : 75.46 % 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: 1.17 (0.35), residues: 554 helix: 1.65 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -0.76 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.007 0.002 HIS A 115 PHE 0.017 0.001 PHE A 117 TYR 0.043 0.002 TYR A 590 ARG 0.011 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.405 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 93 average time/residue: 0.1949 time to fit residues: 21.8756 Evaluate side-chains 89 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.445 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0419 time to fit residues: 1.0039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 50.0000 chunk 49 optimal weight: 0.0980 chunk 51 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7347 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4178 Z= 0.227 Angle : 0.677 9.441 5676 Z= 0.322 Chirality : 0.040 0.181 673 Planarity : 0.004 0.051 698 Dihedral : 5.295 55.951 654 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.04 % Allowed : 24.02 % Favored : 74.93 % 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: 1.17 (0.35), residues: 554 helix: 1.64 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -0.72 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 259 HIS 0.005 0.001 HIS A 115 PHE 0.025 0.001 PHE A 117 TYR 0.040 0.002 TYR A 590 ARG 0.013 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.375 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 88 average time/residue: 0.1716 time to fit residues: 18.3758 Evaluate side-chains 83 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0371 time to fit residues: 0.5783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.5980 chunk 47 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7330 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4178 Z= 0.209 Angle : 0.683 9.444 5676 Z= 0.320 Chirality : 0.040 0.181 673 Planarity : 0.004 0.056 698 Dihedral : 5.299 56.041 654 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.52 % Allowed : 25.07 % Favored : 74.41 % 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: 1.35 (0.35), residues: 554 helix: 1.75 (0.27), residues: 347 sheet: None (None), residues: 0 loop : -0.56 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 171 HIS 0.002 0.001 HIS A 115 PHE 0.012 0.001 PHE A 73 TYR 0.041 0.002 TYR A 590 ARG 0.014 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.517 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 82 average time/residue: 0.1856 time to fit residues: 18.7573 Evaluate side-chains 83 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 0.328 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0366 time to fit residues: 0.6054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.7591 > 50: distance: 65 - 70: 7.915 distance: 66 - 94: 26.807 distance: 70 - 71: 9.373 distance: 71 - 72: 10.890 distance: 71 - 74: 5.588 distance: 72 - 73: 25.553 distance: 72 - 78: 11.363 distance: 73 - 102: 26.232 distance: 74 - 75: 16.462 distance: 74 - 76: 7.476 distance: 75 - 77: 25.143 distance: 78 - 79: 10.312 distance: 79 - 80: 20.705 distance: 79 - 82: 18.800 distance: 80 - 81: 20.226 distance: 80 - 85: 36.132 distance: 82 - 83: 19.119 distance: 82 - 84: 31.127 distance: 85 - 86: 22.992 distance: 86 - 87: 19.704 distance: 86 - 89: 18.132 distance: 87 - 88: 16.149 distance: 87 - 94: 8.875 distance: 89 - 90: 13.011 distance: 90 - 91: 35.065 distance: 91 - 92: 23.101 distance: 92 - 93: 35.521 distance: 94 - 95: 8.853 distance: 95 - 96: 12.465 distance: 95 - 98: 19.608 distance: 96 - 97: 7.406 distance: 96 - 102: 15.026 distance: 98 - 99: 10.727 distance: 98 - 100: 39.791 distance: 99 - 101: 13.439 distance: 102 - 103: 5.742 distance: 103 - 104: 14.911 distance: 103 - 106: 15.290 distance: 104 - 105: 13.329 distance: 104 - 109: 17.481 distance: 106 - 107: 30.050 distance: 106 - 108: 16.355 distance: 109 - 110: 7.823 distance: 110 - 111: 29.291 distance: 110 - 113: 11.910 distance: 111 - 112: 15.835 distance: 111 - 118: 21.233 distance: 113 - 114: 14.295 distance: 114 - 115: 21.843 distance: 115 - 116: 3.270 distance: 115 - 117: 21.345 distance: 118 - 119: 14.218 distance: 118 - 124: 27.547 distance: 119 - 120: 13.259 distance: 119 - 122: 8.782 distance: 120 - 121: 15.980 distance: 120 - 125: 9.605 distance: 122 - 123: 32.319 distance: 123 - 124: 22.801 distance: 125 - 126: 20.836 distance: 126 - 127: 7.603 distance: 126 - 129: 25.483 distance: 127 - 128: 23.358 distance: 127 - 134: 15.657 distance: 129 - 130: 12.348 distance: 131 - 132: 22.869 distance: 131 - 133: 40.926 distance: 134 - 135: 10.024 distance: 135 - 136: 3.096 distance: 135 - 138: 12.466 distance: 136 - 137: 40.763 distance: 136 - 142: 22.533 distance: 138 - 139: 17.775 distance: 139 - 140: 9.914 distance: 139 - 141: 40.993 distance: 142 - 143: 14.094 distance: 143 - 144: 6.005 distance: 143 - 146: 25.660 distance: 144 - 145: 13.082 distance: 144 - 151: 6.750 distance: 145 - 167: 5.522 distance: 146 - 147: 20.253 distance: 147 - 148: 14.045 distance: 148 - 149: 11.613 distance: 149 - 150: 39.820