Starting phenix.real_space_refine on Wed Mar 20 10:13:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbg_25798/03_2024/7tbg_25798.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbg_25798/03_2024/7tbg_25798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbg_25798/03_2024/7tbg_25798.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbg_25798/03_2024/7tbg_25798.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbg_25798/03_2024/7tbg_25798.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbg_25798/03_2024/7tbg_25798.pdb" } resolution = 2.5 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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7528 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 S 44 5.16 5 Na 1 4.78 5 C 6532 2.51 5 N 1510 2.21 5 O 1730 1.98 5 H 9858 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 269": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19679 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 9807 Classifications: {'peptide': 595} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 578} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 9807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 9807 Classifications: {'peptide': 595} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 578} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 36 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 24 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 9.18, per 1000 atoms: 0.47 Number of scatterers: 19679 At special positions: 0 Unit cell: (111.055, 86.005, 106.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 44 16.00 Na 1 11.00 O 1730 8.00 N 1510 7.00 C 6532 6.00 H 9858 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 101 " distance=2.04 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: 15.83 Conformation dependent library (CDL) restraints added in 2.1 seconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 0 sheets defined 84.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 Processing helix chain 'A' and resid 29 through 43 Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 58 through 70 Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 85 through 88 removed outlier: 3.811A pdb=" N GLU A 88 " --> pdb=" O ASN A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 85 through 88' Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.609A pdb=" N GLU A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 95' Processing helix chain 'A' and resid 116 through 137 Processing helix chain 'A' and resid 138 through 141 Processing helix chain 'A' and resid 143 through 150 removed outlier: 3.578A pdb=" N SER A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 172 removed outlier: 3.980A pdb=" N ASP A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.549A pdb=" N VAL A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 238 removed outlier: 3.552A pdb=" N GLY A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLY A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 280 through 295 removed outlier: 4.224A pdb=" N PHE A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 335 Processing helix chain 'A' and resid 343 through 356 Processing helix chain 'A' and resid 384 through 399 removed outlier: 3.798A pdb=" N ALA A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 452 removed outlier: 3.987A pdb=" N GLY A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 487 Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 494 through 511 removed outlier: 3.881A pdb=" N PHE A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 539 removed outlier: 3.870A pdb=" N LEU A 533 " --> pdb=" O TRP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 548 through 565 removed outlier: 4.719A pdb=" N ALA A 553 " --> pdb=" O GLN A 549 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) Proline residue: A 563 - end of helix Processing helix chain 'A' and resid 565 through 588 Processing helix chain 'A' and resid 597 through 601 Processing helix chain 'A' and resid 615 through 628 Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.776A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 648 through 660 removed outlier: 4.165A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 686 Processing helix chain 'B' and resid 21 through 28 Processing helix chain 'B' and resid 29 through 43 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 56 through 70 removed outlier: 4.306A pdb=" N SER B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 90 through 95 removed outlier: 3.562A pdb=" N GLU B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 95' Processing helix chain 'B' and resid 116 through 137 Processing helix chain 'B' and resid 138 through 141 Processing helix chain 'B' and resid 143 through 149 Processing helix chain 'B' and resid 150 through 172 removed outlier: 3.653A pdb=" N ASP B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.503A pdb=" N ILE B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 238 removed outlier: 3.604A pdb=" N MET B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLY B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N THR B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 250 through 263 removed outlier: 3.559A pdb=" N THR B 263 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 280 through 295 removed outlier: 4.202A pdb=" N PHE B 284 " --> pdb=" O TRP B 280 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 335 Processing helix chain 'B' and resid 343 through 356 removed outlier: 3.665A pdb=" N LYS B 349 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 398 removed outlier: 3.765A pdb=" N ALA B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 452 removed outlier: 4.247A pdb=" N GLY B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 487 Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 494 through 511 removed outlier: 3.980A pdb=" N PHE B 499 " --> pdb=" O GLY B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 539 removed outlier: 3.549A pdb=" N LEU B 533 " --> pdb=" O TRP B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 548 through 565 removed outlier: 4.613A pdb=" N ALA B 553 " --> pdb=" O GLN B 549 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N PHE B 554 " --> pdb=" O ARG B 550 " (cutoff:3.500A) Proline residue: B 563 - end of helix Processing helix chain 'B' and resid 565 through 588 Processing helix chain 'B' and resid 597 through 601 Processing helix chain 'B' and resid 615 through 628 Processing helix chain 'B' and resid 632 through 644 removed outlier: 3.760A pdb=" N MET B 636 " --> pdb=" O TRP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' Processing helix chain 'B' and resid 648 through 660 removed outlier: 4.137A pdb=" N PHE B 652 " --> pdb=" O SER B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 686 682 hydrogen bonds defined for protein. 1998 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: 7.11 Time building geometry restraints manager: 16.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 9846 1.02 - 1.22: 12 1.22 - 1.42: 4376 1.42 - 1.62: 5604 1.62 - 1.82: 72 Bond restraints: 19910 Sorted by residual: bond pdb=" ND2 ASN B 631 " pdb="HD22 ASN B 631 " ideal model delta sigma weight residual 0.860 0.819 0.041 2.00e-02 2.50e+03 4.15e+00 bond pdb=" CB PRO A 99 " pdb=" CG PRO A 99 " ideal model delta sigma weight residual 1.506 1.437 0.069 3.90e-02 6.57e+02 3.16e+00 bond pdb=" CB PRO B 99 " pdb=" CG PRO B 99 " ideal model delta sigma weight residual 1.506 1.439 0.067 3.90e-02 6.57e+02 2.95e+00 bond pdb=" N ARG A 20 " pdb=" CA ARG A 20 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.65e+00 bond pdb=" N ARG B 20 " pdb=" CA ARG B 20 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.53e+00 ... (remaining 19905 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.18: 692 107.18 - 113.91: 22435 113.91 - 120.63: 7930 120.63 - 127.36: 4688 127.36 - 134.09: 103 Bond angle restraints: 35848 Sorted by residual: angle pdb=" N ASN B 96 " pdb=" CA ASN B 96 " pdb=" C ASN B 96 " ideal model delta sigma weight residual 109.81 116.42 -6.61 2.21e+00 2.05e-01 8.94e+00 angle pdb=" CA TRP B 271 " pdb=" CB TRP B 271 " pdb=" CG TRP B 271 " ideal model delta sigma weight residual 113.60 119.25 -5.65 1.90e+00 2.77e-01 8.86e+00 angle pdb=" CA TRP A 271 " pdb=" CB TRP A 271 " pdb=" CG TRP A 271 " ideal model delta sigma weight residual 113.60 119.14 -5.54 1.90e+00 2.77e-01 8.49e+00 angle pdb=" N ASN A 96 " pdb=" CA ASN A 96 " pdb=" C ASN A 96 " ideal model delta sigma weight residual 109.81 115.84 -6.03 2.21e+00 2.05e-01 7.44e+00 angle pdb="HD21 ASN B 631 " pdb=" ND2 ASN B 631 " pdb="HD22 ASN B 631 " ideal model delta sigma weight residual 120.00 111.82 8.18 3.00e+00 1.11e-01 7.44e+00 ... (remaining 35843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8579 17.87 - 35.74: 462 35.74 - 53.61: 141 53.61 - 71.48: 156 71.48 - 89.35: 6 Dihedral angle restraints: 9344 sinusoidal: 4854 harmonic: 4490 Sorted by residual: dihedral pdb=" CA GLU B 600 " pdb=" C GLU B 600 " pdb=" N THR B 601 " pdb=" CA THR B 601 " ideal model delta harmonic sigma weight residual -180.00 -150.60 -29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ARG A 20 " pdb=" C ARG A 20 " pdb=" N ARG A 21 " pdb=" CA ARG A 21 " ideal model delta harmonic sigma weight residual -180.00 -152.08 -27.92 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA GLU A 600 " pdb=" C GLU A 600 " pdb=" N THR A 601 " pdb=" CA THR A 601 " ideal model delta harmonic sigma weight residual 180.00 -152.18 -27.82 0 5.00e+00 4.00e-02 3.10e+01 ... (remaining 9341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 845 0.035 - 0.069: 527 0.069 - 0.104: 126 0.104 - 0.139: 43 0.139 - 0.173: 13 Chirality restraints: 1554 Sorted by residual: chirality pdb=" CA TRP B 271 " pdb=" N TRP B 271 " pdb=" C TRP B 271 " pdb=" CB TRP B 271 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA PRO B 30 " pdb=" N PRO B 30 " pdb=" C PRO B 30 " pdb=" CB PRO B 30 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA GLU A 42 " pdb=" N GLU A 42 " pdb=" C GLU A 42 " pdb=" CB GLU A 42 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 1551 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 631 " -0.064 2.00e-02 2.50e+03 8.18e-02 1.00e+02 pdb=" CG ASN B 631 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN B 631 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 631 " 0.130 2.00e-02 2.50e+03 pdb="HD21 ASN B 631 " 0.013 2.00e-02 2.50e+03 pdb="HD22 ASN B 631 " -0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 631 " -0.052 2.00e-02 2.50e+03 6.58e-02 6.49e+01 pdb=" CG ASN A 631 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN A 631 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 631 " 0.105 2.00e-02 2.50e+03 pdb="HD21 ASN A 631 " 0.006 2.00e-02 2.50e+03 pdb="HD22 ASN A 631 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 191 " 0.227 9.50e-02 1.11e+02 7.99e-02 2.04e+01 pdb=" NE ARG B 191 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 191 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG B 191 " -0.040 2.00e-02 2.50e+03 pdb=" NH2 ARG B 191 " -0.034 2.00e-02 2.50e+03 pdb="HH11 ARG B 191 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 191 " 0.032 2.00e-02 2.50e+03 pdb="HH21 ARG B 191 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 191 " 0.034 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 645 2.14 - 2.76: 36495 2.76 - 3.37: 56344 3.37 - 3.99: 70418 3.99 - 4.60: 110815 Nonbonded interactions: 274717 Sorted by model distance: nonbonded pdb=" O THR A 263 " pdb=" HG1 THR A 264 " model vdw 1.526 1.850 nonbonded pdb=" HG1 THR B 452 " pdb=" OD1 ASN B 454 " model vdw 1.582 1.850 nonbonded pdb=" O TYR B 491 " pdb="HD22 ASN B 497 " model vdw 1.584 1.850 nonbonded pdb=" HG1 THR A 452 " pdb=" OD1 ASN A 454 " model vdw 1.588 1.850 nonbonded pdb=" O THR B 263 " pdb=" HG1 THR B 264 " model vdw 1.598 1.850 ... (remaining 274712 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 686 or resid 801 through 802)) selection = chain 'B' } 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: 5.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.270 Extract box with map and model: 12.870 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 64.210 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 : 0.006 0.069 10052 Z= 0.385 Angle : 0.759 6.607 13662 Z= 0.470 Chirality : 0.047 0.173 1554 Planarity : 0.009 0.133 1670 Dihedral : 13.033 89.345 3526 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.57 % Allowed : 4.53 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.60 (0.24), residues: 1166 helix: 0.18 (0.16), residues: 862 sheet: None (None), residues: 0 loop : 1.66 (0.44), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP A 271 HIS 0.004 0.001 HIS A 134 PHE 0.021 0.003 PHE B 599 TYR 0.026 0.006 TYR A 608 ARG 0.018 0.003 ARG B 279 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 280 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 274 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.6807 (t0) cc_final: 0.6516 (t0) REVERT: A 399 PHE cc_start: 0.5522 (t80) cc_final: 0.5289 (t80) REVERT: A 629 MET cc_start: 0.8585 (mmm) cc_final: 0.8217 (mmp) REVERT: A 681 LEU cc_start: 0.8463 (tt) cc_final: 0.8254 (tp) REVERT: A 683 GLU cc_start: 0.6895 (tm-30) cc_final: 0.6497 (tm-30) REVERT: B 147 PHE cc_start: 0.8078 (t80) cc_final: 0.7768 (t80) REVERT: B 629 MET cc_start: 0.8561 (mmm) cc_final: 0.8352 (mmp) outliers start: 6 outliers final: 2 residues processed: 278 average time/residue: 2.7856 time to fit residues: 824.7654 Evaluate side-chains 221 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 219 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain B residue 57 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 0.0870 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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: 0.7623 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10052 Z= 0.275 Angle : 0.581 5.905 13662 Z= 0.317 Chirality : 0.039 0.143 1554 Planarity : 0.004 0.047 1670 Dihedral : 4.951 27.384 1297 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.26 % Allowed : 11.51 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1.98 (0.25), residues: 1166 helix: 1.34 (0.17), residues: 878 sheet: None (None), residues: 0 loop : 1.64 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 271 HIS 0.003 0.001 HIS A 134 PHE 0.017 0.002 PHE B 599 TYR 0.022 0.002 TYR B 141 ARG 0.005 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 252 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 228 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.6832 (t0) cc_final: 0.6488 (t0) REVERT: A 399 PHE cc_start: 0.5799 (t80) cc_final: 0.5509 (t80) REVERT: A 560 THR cc_start: 0.8379 (t) cc_final: 0.8166 (p) REVERT: A 629 MET cc_start: 0.8661 (mmm) cc_final: 0.8377 (mmp) REVERT: A 681 LEU cc_start: 0.8483 (tt) cc_final: 0.8269 (tp) REVERT: B 225 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8389 (mp) REVERT: B 325 ARG cc_start: 0.7364 (ttm-80) cc_final: 0.7130 (ttp-170) REVERT: B 585 GLN cc_start: 0.7553 (tm-30) cc_final: 0.7329 (tm-30) REVERT: B 615 ASP cc_start: 0.7176 (t0) cc_final: 0.6959 (t0) REVERT: B 629 MET cc_start: 0.8617 (mmm) cc_final: 0.8400 (mmp) outliers start: 24 outliers final: 13 residues processed: 237 average time/residue: 2.6849 time to fit residues: 679.7122 Evaluate side-chains 244 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 230 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 601 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 106 optimal weight: 0.0980 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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: 0.7634 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10052 Z= 0.297 Angle : 0.551 5.269 13662 Z= 0.299 Chirality : 0.038 0.142 1554 Planarity : 0.004 0.042 1670 Dihedral : 4.670 25.089 1296 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.26 % Allowed : 12.83 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.25), residues: 1166 helix: 1.55 (0.17), residues: 878 sheet: None (None), residues: 0 loop : 1.56 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 271 HIS 0.003 0.001 HIS B 134 PHE 0.018 0.002 PHE B 599 TYR 0.023 0.002 TYR B 141 ARG 0.006 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 253 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 229 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7004 (mm-30) REVERT: A 78 TYR cc_start: 0.7602 (m-80) cc_final: 0.7118 (m-10) REVERT: A 399 PHE cc_start: 0.5828 (t80) cc_final: 0.5476 (t80) REVERT: A 629 MET cc_start: 0.8598 (mmm) cc_final: 0.8369 (mmp) REVERT: A 681 LEU cc_start: 0.8497 (tt) cc_final: 0.8271 (tp) REVERT: A 683 GLU cc_start: 0.6954 (tm-30) cc_final: 0.6652 (tm-30) REVERT: B 225 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8428 (mp) REVERT: B 325 ARG cc_start: 0.7361 (ttm-80) cc_final: 0.7079 (ttm-80) REVERT: B 560 THR cc_start: 0.8387 (t) cc_final: 0.8134 (p) REVERT: B 585 GLN cc_start: 0.7562 (tm-30) cc_final: 0.7353 (tm-30) REVERT: B 629 MET cc_start: 0.8548 (mmm) cc_final: 0.8219 (mmp) outliers start: 24 outliers final: 12 residues processed: 235 average time/residue: 2.9019 time to fit residues: 724.8710 Evaluate side-chains 241 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 228 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 601 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 11 optimal weight: 0.0970 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 107 optimal weight: 0.3980 chunk 114 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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: 0.7625 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10052 Z= 0.241 Angle : 0.513 4.946 13662 Z= 0.279 Chirality : 0.037 0.140 1554 Planarity : 0.004 0.046 1670 Dihedral : 4.436 22.238 1296 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.36 % Allowed : 12.74 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.25), residues: 1166 helix: 1.70 (0.17), residues: 890 sheet: None (None), residues: 0 loop : 1.42 (0.45), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 271 HIS 0.003 0.001 HIS B 134 PHE 0.016 0.001 PHE A 195 TYR 0.020 0.001 TYR B 141 ARG 0.005 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 231 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6970 (mm-30) REVERT: A 43 ASP cc_start: 0.6819 (t0) cc_final: 0.6412 (t0) REVERT: A 78 TYR cc_start: 0.7581 (m-80) cc_final: 0.7038 (m-10) REVERT: A 399 PHE cc_start: 0.5728 (t80) cc_final: 0.5309 (t80) REVERT: A 560 THR cc_start: 0.8331 (t) cc_final: 0.8118 (p) REVERT: A 629 MET cc_start: 0.8565 (mmm) cc_final: 0.8260 (mmp) REVERT: A 681 LEU cc_start: 0.8489 (tt) cc_final: 0.8275 (tp) REVERT: B 225 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8415 (mp) REVERT: B 585 GLN cc_start: 0.7547 (tm-30) cc_final: 0.7316 (tm-30) REVERT: B 629 MET cc_start: 0.8515 (mmm) cc_final: 0.8240 (mmp) outliers start: 25 outliers final: 10 residues processed: 238 average time/residue: 2.7877 time to fit residues: 707.4822 Evaluate side-chains 244 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 233 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 601 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10052 Z= 0.342 Angle : 0.544 5.853 13662 Z= 0.297 Chirality : 0.039 0.149 1554 Planarity : 0.004 0.054 1670 Dihedral : 4.484 23.566 1296 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.26 % Allowed : 13.11 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.25), residues: 1166 helix: 1.66 (0.17), residues: 890 sheet: None (None), residues: 0 loop : 1.24 (0.44), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 271 HIS 0.003 0.001 HIS B 134 PHE 0.020 0.002 PHE B 599 TYR 0.025 0.002 TYR B 141 ARG 0.006 0.000 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 227 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6972 (mm-30) REVERT: A 399 PHE cc_start: 0.5800 (t80) cc_final: 0.5325 (t80) REVERT: A 629 MET cc_start: 0.8514 (mmm) cc_final: 0.8185 (mmp) REVERT: A 681 LEU cc_start: 0.8519 (tt) cc_final: 0.8272 (tp) REVERT: A 683 GLU cc_start: 0.6965 (tm-30) cc_final: 0.6686 (tm-30) REVERT: B 225 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8431 (mp) REVERT: B 560 THR cc_start: 0.8370 (t) cc_final: 0.8104 (p) REVERT: B 585 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7379 (tm-30) REVERT: B 615 ASP cc_start: 0.7226 (t0) cc_final: 0.6999 (t0) outliers start: 24 outliers final: 19 residues processed: 238 average time/residue: 2.7526 time to fit residues: 698.8921 Evaluate side-chains 246 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 226 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 601 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 0.0470 chunk 28 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN B 315 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10052 Z= 0.275 Angle : 0.517 5.525 13662 Z= 0.282 Chirality : 0.037 0.143 1554 Planarity : 0.004 0.051 1670 Dihedral : 4.387 22.477 1296 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.08 % Allowed : 13.68 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.25), residues: 1166 helix: 1.78 (0.17), residues: 890 sheet: None (None), residues: 0 loop : 1.12 (0.44), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 271 HIS 0.002 0.001 HIS B 134 PHE 0.019 0.001 PHE A 147 TYR 0.021 0.002 TYR B 141 ARG 0.008 0.000 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 229 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6969 (mm-30) REVERT: A 399 PHE cc_start: 0.5834 (t80) cc_final: 0.5322 (t80) REVERT: A 494 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6499 (mt-10) REVERT: A 560 THR cc_start: 0.8324 (t) cc_final: 0.8101 (p) REVERT: A 629 MET cc_start: 0.8504 (mmm) cc_final: 0.8238 (mmp) REVERT: B 225 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8430 (mp) REVERT: B 585 GLN cc_start: 0.7574 (tm-30) cc_final: 0.7356 (tm-30) REVERT: B 615 ASP cc_start: 0.7189 (t0) cc_final: 0.6971 (t0) outliers start: 22 outliers final: 13 residues processed: 239 average time/residue: 2.7489 time to fit residues: 701.2204 Evaluate side-chains 239 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 225 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 601 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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: 64.5474 > 50: distance: 220 - 232: 13.061 distance: 232 - 233: 6.735 distance: 232 - 238: 9.733 distance: 233 - 234: 19.108 distance: 233 - 236: 18.747 distance: 233 - 239: 6.029 distance: 234 - 235: 11.896 distance: 234 - 246: 29.591 distance: 236 - 240: 20.440 distance: 236 - 241: 10.980 distance: 237 - 238: 15.186 distance: 237 - 242: 9.017 distance: 237 - 243: 6.510 distance: 238 - 244: 19.306 distance: 238 - 245: 14.084 distance: 246 - 247: 12.654 distance: 246 - 254: 21.072 distance: 247 - 248: 5.817 distance: 247 - 250: 26.700 distance: 247 - 255: 9.728 distance: 248 - 249: 23.289 distance: 248 - 258: 9.433 distance: 250 - 251: 3.928 distance: 250 - 256: 12.537 distance: 250 - 257: 15.618 distance: 251 - 252: 22.844 distance: 251 - 253: 17.111 distance: 258 - 259: 11.736 distance: 258 - 265: 25.646 distance: 259 - 260: 14.134 distance: 259 - 262: 18.887 distance: 259 - 266: 5.134 distance: 260 - 261: 9.322 distance: 260 - 274: 27.828 distance: 262 - 263: 15.812 distance: 262 - 264: 6.447 distance: 262 - 267: 10.067 distance: 263 - 268: 8.554 distance: 263 - 269: 5.044 distance: 263 - 270: 9.009 distance: 264 - 271: 14.568 distance: 264 - 272: 13.701 distance: 264 - 273: 19.302 distance: 274 - 275: 10.904 distance: 275 - 276: 6.909 distance: 275 - 278: 4.079 distance: 275 - 289: 8.571 distance: 276 - 277: 7.872 distance: 276 - 298: 16.491 distance: 277 - 341: 7.586 distance: 278 - 279: 6.365 distance: 278 - 290: 8.726 distance: 278 - 291: 7.343 distance: 279 - 280: 3.156 distance: 279 - 281: 3.421 distance: 280 - 292: 3.316 distance: 281 - 283: 3.715 distance: 282 - 293: 3.197 distance: 284 - 294: 4.936 distance: 285 - 295: 4.493 distance: 298 - 299: 29.840 distance: 298 - 306: 14.909 distance: 299 - 300: 25.486 distance: 299 - 302: 32.551 distance: 299 - 307: 12.484 distance: 300 - 301: 11.615 distance: 300 - 317: 16.342 distance: 301 - 362: 3.306 distance: 302 - 303: 27.766 distance: 302 - 304: 16.600 distance: 302 - 308: 18.547 distance: 303 - 309: 5.955 distance: 303 - 310: 3.541 distance: 304 - 311: 3.689 distance: 304 - 312: 4.881 distance: 304 - 313: 10.761 distance: 305 - 314: 10.065 distance: 305 - 315: 9.229 distance: 317 - 318: 7.428 distance: 317 - 323: 9.606 distance: 318 - 319: 4.187 distance: 318 - 321: 7.970 distance: 318 - 324: 17.053 distance: 319 - 320: 9.279 distance: 319 - 331: 12.109 distance: 320 - 384: 11.640 distance: 321 - 322: 5.385 distance: 321 - 325: 12.947 distance: 321 - 326: 5.753 distance: 322 - 323: 6.655 distance: 322 - 327: 5.366 distance: 322 - 328: 7.864 distance: 323 - 329: 18.553 distance: 323 - 330: 3.861 distance: 331 - 332: 13.874 distance: 331 - 336: 16.443 distance: 332 - 333: 7.388 distance: 332 - 335: 10.787 distance: 332 - 337: 3.196 distance: 333 - 334: 6.221 distance: 334 - 395: 13.066 distance: 335 - 338: 16.163 distance: 335 - 339: 15.922 distance: 335 - 340: 18.540 distance: 341 - 342: 5.705 distance: 341 - 353: 18.827 distance: 342 - 343: 6.578 distance: 342 - 345: 9.341 distance: 342 - 354: 11.131 distance: 343 - 344: 5.040 distance: 343 - 362: 13.595 distance: 345 - 346: 6.984 distance: 345 - 355: 12.582 distance: 345 - 356: 7.596 distance: 347 - 357: 4.376 distance: 349 - 351: 5.729 distance: 349 - 359: 7.022 distance: 350 - 351: 4.470 distance: 350 - 360: 3.091 distance: 351 - 352: 9.160 distance: 362 - 363: 20.507 distance: 362 - 371: 21.790 distance: 363 - 364: 10.634 distance: 363 - 366: 18.301 distance: 363 - 372: 7.467 distance: 364 - 365: 29.912 distance: 364 - 384: 13.207 distance: 366 - 367: 31.908 distance: 366 - 373: 23.200 distance: 366 - 374: 14.419 distance: 367 - 368: 37.545 distance: 367 - 375: 20.338 distance: 367 - 376: 24.424 distance: 368 - 369: 5.384 distance: 368 - 377: 16.141 distance: 368 - 378: 23.116 distance: 369 - 370: 15.823 distance: 369 - 379: 5.655 distance: 369 - 380: 3.442 distance: 370 - 381: 11.394 distance: 370 - 382: 13.534 distance: 370 - 383: 4.735 distance: 384 - 385: 10.644 distance: 384 - 390: 25.720 distance: 385 - 386: 7.568 distance: 385 - 388: 3.387 distance: 385 - 391: 8.020 distance: 386 - 387: 4.342 distance: 388 - 389: 11.201 distance: 388 - 392: 11.590 distance: 388 - 393: 11.735 distance: 389 - 394: 8.145