Starting phenix.real_space_refine on Fri Aug 2 23:39:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9p_26404/08_2024/7u9p_26404.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9p_26404/08_2024/7u9p_26404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9p_26404/08_2024/7u9p_26404.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9p_26404/08_2024/7u9p_26404.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9p_26404/08_2024/7u9p_26404.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9p_26404/08_2024/7u9p_26404.cif" } resolution = 3.5 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= 0.000 sd= 0.002 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 23 5.16 5 C 3920 2.51 5 N 1005 2.21 5 O 1178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 58": "NH1" <-> "NH2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 142": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6126 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2116 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 16, 'TRANS': 251} Chain breaks: 1 Chain: "B" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1507 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 10, 'TRANS': 173} Chain breaks: 9 Chain: "H" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1274 Classifications: {'peptide': 168} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 159} Chain breaks: 3 Chain: "L" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1173 Classifications: {'peptide': 153} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 142} Chain breaks: 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 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.15, per 1000 atoms: 0.68 Number of scatterers: 6126 At special positions: 0 Unit cell: (78.57, 89.046, 123.093, 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 23 16.00 O 1178 8.00 N 1005 7.00 C 3920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 107 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 16 sheets defined 4.1% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.635A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.052A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.973A pdb=" N SER H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.236A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL A 395 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER A 514 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA A 397 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 512 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER A 399 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL A 510 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N VAL A 401 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TYR A 508 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.236A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N ASN A 394 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 10.742A pdb=" N ALA A 522 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 540 removed outlier: 3.624A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.263A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AA7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.521A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.575A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 224 through 229 removed outlier: 5.995A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.565A pdb=" N LEU H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER H 25 " --> pdb=" O LEU H 3 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU H 5 " --> pdb=" O GLU H 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.846A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.866A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 149 through 150 removed outlier: 3.635A pdb=" N SER H 190 " --> pdb=" O CYS H 150 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.931A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.576A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 114 through 115 129 hydrogen bonds defined for protein. 309 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: 1.67 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1790 1.33 - 1.46: 1646 1.46 - 1.58: 2808 1.58 - 1.71: 0 1.71 - 1.84: 27 Bond restraints: 6271 Sorted by residual: bond pdb=" CB ARG A 509 " pdb=" CG ARG A 509 " ideal model delta sigma weight residual 1.520 1.423 0.097 3.00e-02 1.11e+03 1.04e+01 bond pdb=" C VAL A 433 " pdb=" N ILE A 434 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.42e-02 4.96e+03 7.18e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" CG MET L 4 " pdb=" SD MET L 4 " ideal model delta sigma weight residual 1.803 1.743 0.060 2.50e-02 1.60e+03 5.73e+00 bond pdb=" CA SER A 494 " pdb=" CB SER A 494 " ideal model delta sigma weight residual 1.532 1.492 0.040 1.74e-02 3.30e+03 5.22e+00 ... (remaining 6266 not shown) Histogram of bond angle deviations from ideal: 96.07 - 103.68: 103 103.68 - 111.28: 2449 111.28 - 118.88: 2375 118.88 - 126.48: 3500 126.48 - 134.09: 83 Bond angle restraints: 8510 Sorted by residual: angle pdb=" N LYS L 169 " pdb=" CA LYS L 169 " pdb=" C LYS L 169 " ideal model delta sigma weight residual 114.04 106.50 7.54 1.24e+00 6.50e-01 3.69e+01 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 126.65 -12.25 2.30e+00 1.89e-01 2.84e+01 angle pdb=" C CYS H 107 " pdb=" N ASP H 108 " pdb=" CA ASP H 108 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C SER B 31 " pdb=" N PHE B 32 " pdb=" CA PHE B 32 " ideal model delta sigma weight residual 121.54 130.88 -9.34 1.91e+00 2.74e-01 2.39e+01 angle pdb=" N ALA H 109 " pdb=" CA ALA H 109 " pdb=" C ALA H 109 " ideal model delta sigma weight residual 108.02 99.93 8.09 1.78e+00 3.16e-01 2.06e+01 ... (remaining 8505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 3540 16.49 - 32.98: 171 32.98 - 49.47: 38 49.47 - 65.96: 1 65.96 - 82.45: 4 Dihedral angle restraints: 3754 sinusoidal: 1516 harmonic: 2238 Sorted by residual: dihedral pdb=" CB CYS H 102 " pdb=" SG CYS H 102 " pdb=" SG CYS H 107 " pdb=" CB CYS H 107 " ideal model delta sinusoidal sigma weight residual 93.00 161.76 -68.76 1 1.00e+01 1.00e-02 6.12e+01 dihedral pdb=" CA CYS A 525 " pdb=" C CYS A 525 " pdb=" N GLY A 526 " pdb=" CA GLY A 526 " ideal model delta harmonic sigma weight residual -180.00 -154.48 -25.52 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA GLU L 143 " pdb=" C GLU L 143 " pdb=" N ALA L 144 " pdb=" CA ALA L 144 " ideal model delta harmonic sigma weight residual -180.00 -156.66 -23.34 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 3751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 643 0.062 - 0.124: 260 0.124 - 0.185: 38 0.185 - 0.247: 10 0.247 - 0.309: 2 Chirality restraints: 953 Sorted by residual: chirality pdb=" CG LEU L 33 " pdb=" CB LEU L 33 " pdb=" CD1 LEU L 33 " pdb=" CD2 LEU L 33 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA ASP H 108 " pdb=" N ASP H 108 " pdb=" C ASP H 108 " pdb=" CB ASP H 108 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CB VAL A 350 " pdb=" CA VAL A 350 " pdb=" CG1 VAL A 350 " pdb=" CG2 VAL A 350 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 950 not shown) Planarity restraints: 1087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.81e+00 pdb=" N PRO A 463 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 113 " 0.027 2.00e-02 2.50e+03 1.73e-02 7.49e+00 pdb=" CG TRP H 113 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP H 113 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP H 113 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP H 113 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP H 113 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 113 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 113 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 113 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 113 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA L 43 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO L 44 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO L 44 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 44 " -0.036 5.00e-02 4.00e+02 ... (remaining 1084 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1907 2.82 - 3.34: 4660 3.34 - 3.86: 9200 3.86 - 4.38: 9990 4.38 - 4.90: 18434 Nonbonded interactions: 44191 Sorted by model distance: nonbonded pdb=" OD1 ASN A 394 " pdb=" OH TYR B 200 " model vdw 2.304 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.342 3.040 nonbonded pdb=" OH TYR A 351 " pdb=" NE2 HIS H 101 " model vdw 2.347 3.120 nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.351 3.040 nonbonded pdb=" NH2 ARG A 454 " pdb=" O ASP A 467 " model vdw 2.352 3.120 ... (remaining 44186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.500 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.102 6271 Z= 0.826 Angle : 1.181 12.250 8510 Z= 0.645 Chirality : 0.067 0.309 953 Planarity : 0.009 0.074 1083 Dihedral : 10.398 82.447 2290 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.56 % Favored : 88.16 % Rotamer: Outliers : 0.15 % Allowed : 3.54 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -4.34 (0.25), residues: 735 helix: -4.63 (0.62), residues: 18 sheet: -2.25 (0.31), residues: 238 loop : -3.34 (0.22), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.006 TRP H 113 HIS 0.008 0.002 HIS H 35 PHE 0.041 0.005 PHE A 347 TYR 0.042 0.005 TYR H 94 ARG 0.016 0.002 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 0.754 Fit side-chains REVERT: A 414 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7967 (mm-40) REVERT: A 564 GLN cc_start: 0.7891 (mt0) cc_final: 0.7689 (mt0) REVERT: B 281 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8388 (tm-30) REVERT: L 108 ARG cc_start: 0.7466 (ptm-80) cc_final: 0.7153 (ptm160) outliers start: 1 outliers final: 1 residues processed: 122 average time/residue: 0.2376 time to fit residues: 36.0021 Evaluate side-chains 100 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.6980 chunk 56 optimal weight: 30.0000 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.0770 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN H 39 GLN H 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6271 Z= 0.172 Angle : 0.599 9.045 8510 Z= 0.312 Chirality : 0.044 0.226 953 Planarity : 0.005 0.054 1083 Dihedral : 5.487 22.921 915 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.92 % Allowed : 7.37 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.27), residues: 735 helix: -4.56 (0.52), residues: 20 sheet: -1.46 (0.33), residues: 240 loop : -2.87 (0.23), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 436 HIS 0.003 0.001 HIS B 207 PHE 0.015 0.001 PHE A 486 TYR 0.018 0.002 TYR L 140 ARG 0.003 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7957 (mm110) REVERT: A 515 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.8226 (p90) REVERT: B 32 PHE cc_start: 0.6505 (OUTLIER) cc_final: 0.5854 (m-10) REVERT: H 110 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.8218 (p90) REVERT: L 108 ARG cc_start: 0.7357 (ptm-80) cc_final: 0.7045 (ptm160) outliers start: 13 outliers final: 7 residues processed: 112 average time/residue: 0.2086 time to fit residues: 29.8636 Evaluate side-chains 105 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6271 Z= 0.167 Angle : 0.555 7.243 8510 Z= 0.285 Chirality : 0.043 0.148 953 Planarity : 0.005 0.041 1083 Dihedral : 4.810 19.703 914 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.95 % Allowed : 8.26 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -2.99 (0.28), residues: 735 helix: -3.85 (0.84), residues: 14 sheet: -1.03 (0.35), residues: 232 loop : -2.58 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.002 0.001 HIS B 207 PHE 0.013 0.001 PHE A 486 TYR 0.017 0.001 TYR L 140 ARG 0.003 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 0.695 Fit side-chains REVERT: A 414 GLN cc_start: 0.8287 (mm-40) cc_final: 0.8000 (mm-40) REVERT: A 515 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8250 (p90) REVERT: B 34 ARG cc_start: 0.8208 (mmm160) cc_final: 0.7955 (mmm-85) REVERT: B 239 GLN cc_start: 0.8477 (tt0) cc_final: 0.8243 (tt0) outliers start: 20 outliers final: 11 residues processed: 117 average time/residue: 0.2101 time to fit residues: 31.1995 Evaluate side-chains 105 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 0.0020 chunk 35 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 64 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 overall best weight: 1.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6271 Z= 0.233 Angle : 0.586 6.746 8510 Z= 0.301 Chirality : 0.044 0.151 953 Planarity : 0.005 0.040 1083 Dihedral : 4.879 18.615 914 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.10 % Allowed : 9.73 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -2.73 (0.28), residues: 735 helix: -3.62 (0.92), residues: 14 sheet: -0.79 (0.35), residues: 233 loop : -2.44 (0.24), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 436 HIS 0.003 0.001 HIS B 207 PHE 0.013 0.002 PHE A 377 TYR 0.017 0.002 TYR L 140 ARG 0.004 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.717 Fit side-chains REVERT: A 414 GLN cc_start: 0.8283 (mm-40) cc_final: 0.8000 (mm-40) REVERT: A 515 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8256 (p90) REVERT: A 538 CYS cc_start: 0.5091 (t) cc_final: 0.4691 (t) REVERT: H 110 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.8219 (p90) outliers start: 21 outliers final: 17 residues processed: 110 average time/residue: 0.2236 time to fit residues: 31.5210 Evaluate side-chains 114 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN B 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6271 Z= 0.185 Angle : 0.552 6.776 8510 Z= 0.282 Chirality : 0.043 0.149 953 Planarity : 0.004 0.039 1083 Dihedral : 4.623 17.714 914 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.54 % Allowed : 10.03 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -2.43 (0.29), residues: 735 helix: -3.45 (0.96), residues: 14 sheet: -0.55 (0.35), residues: 235 loop : -2.25 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 436 HIS 0.002 0.001 HIS B 207 PHE 0.011 0.001 PHE A 486 TYR 0.018 0.001 TYR L 140 ARG 0.006 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 0.702 Fit side-chains REVERT: A 414 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8055 (mm-40) REVERT: A 515 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8300 (p90) REVERT: A 538 CYS cc_start: 0.5068 (t) cc_final: 0.4687 (t) REVERT: B 139 PRO cc_start: 0.8300 (Cg_exo) cc_final: 0.8091 (Cg_endo) REVERT: H 110 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.8182 (p90) outliers start: 24 outliers final: 17 residues processed: 109 average time/residue: 0.1941 time to fit residues: 27.5477 Evaluate side-chains 114 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 6271 Z= 0.403 Angle : 0.670 6.679 8510 Z= 0.347 Chirality : 0.046 0.195 953 Planarity : 0.005 0.045 1083 Dihedral : 5.261 18.213 914 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.12 % Favored : 90.75 % Rotamer: Outliers : 4.42 % Allowed : 10.47 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -2.62 (0.28), residues: 735 helix: -3.55 (0.96), residues: 14 sheet: -0.68 (0.33), residues: 245 loop : -2.41 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 436 HIS 0.004 0.001 HIS B 207 PHE 0.018 0.002 PHE B 86 TYR 0.018 0.002 TYR L 140 ARG 0.004 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 93 time to evaluate : 0.701 Fit side-chains REVERT: A 369 TYR cc_start: 0.7826 (t80) cc_final: 0.7566 (t80) REVERT: A 414 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8057 (mm-40) REVERT: A 515 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8317 (p90) REVERT: A 538 CYS cc_start: 0.5158 (t) cc_final: 0.4774 (t) REVERT: H 110 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8220 (p90) outliers start: 30 outliers final: 21 residues processed: 113 average time/residue: 0.2161 time to fit residues: 31.1248 Evaluate side-chains 116 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 61 optimal weight: 0.0770 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6271 Z= 0.250 Angle : 0.604 9.254 8510 Z= 0.306 Chirality : 0.044 0.172 953 Planarity : 0.004 0.039 1083 Dihedral : 4.978 18.065 914 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.42 % Allowed : 11.50 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -2.42 (0.29), residues: 735 helix: -3.60 (0.94), residues: 14 sheet: -0.51 (0.34), residues: 245 loop : -2.29 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 436 HIS 0.003 0.001 HIS B 207 PHE 0.014 0.002 PHE B 86 TYR 0.020 0.002 TYR L 140 ARG 0.003 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 94 time to evaluate : 0.650 Fit side-chains REVERT: A 369 TYR cc_start: 0.7801 (t80) cc_final: 0.7542 (t80) REVERT: A 414 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8053 (mm-40) REVERT: A 515 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8265 (p90) REVERT: A 538 CYS cc_start: 0.5152 (t) cc_final: 0.4795 (t) REVERT: H 110 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8191 (p90) outliers start: 30 outliers final: 20 residues processed: 113 average time/residue: 0.2172 time to fit residues: 30.9567 Evaluate side-chains 112 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.0570 chunk 6 optimal weight: 0.0010 chunk 56 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 69 optimal weight: 0.0000 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 0.0770 overall best weight: 0.1666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6271 Z= 0.115 Angle : 0.527 9.100 8510 Z= 0.263 Chirality : 0.042 0.140 953 Planarity : 0.004 0.040 1083 Dihedral : 4.210 15.656 914 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.36 % Allowed : 13.42 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -2.00 (0.30), residues: 735 helix: -3.51 (0.82), residues: 20 sheet: -0.23 (0.35), residues: 242 loop : -1.94 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.001 0.000 HIS B 207 PHE 0.008 0.001 PHE B 238 TYR 0.018 0.001 TYR L 140 ARG 0.004 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 0.456 Fit side-chains REVERT: A 414 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8019 (mm-40) REVERT: A 538 CYS cc_start: 0.5014 (t) cc_final: 0.4654 (t) REVERT: B 139 PRO cc_start: 0.8102 (Cg_exo) cc_final: 0.7848 (Cg_endo) REVERT: L 81 GLU cc_start: 0.7573 (pt0) cc_final: 0.7346 (pm20) outliers start: 16 outliers final: 11 residues processed: 117 average time/residue: 0.1469 time to fit residues: 22.0304 Evaluate side-chains 102 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 50.8626 > 50: distance: 18 - 23: 6.113 distance: 23 - 24: 9.057 distance: 24 - 25: 20.962 distance: 24 - 27: 23.460 distance: 25 - 26: 15.429 distance: 25 - 28: 15.713 distance: 28 - 29: 30.464 distance: 29 - 30: 26.989 distance: 29 - 32: 27.584 distance: 30 - 31: 25.693 distance: 30 - 33: 38.090 distance: 33 - 34: 36.840 distance: 33 - 39: 28.169 distance: 34 - 35: 15.205 distance: 34 - 37: 16.523 distance: 35 - 36: 16.456 distance: 35 - 40: 23.174 distance: 37 - 38: 29.936 distance: 38 - 39: 30.704 distance: 40 - 41: 11.937 distance: 40 - 129: 7.663 distance: 41 - 42: 5.823 distance: 41 - 44: 13.745 distance: 42 - 43: 9.438 distance: 42 - 46: 8.903 distance: 43 - 126: 7.560 distance: 44 - 45: 5.454 distance: 46 - 47: 3.669 distance: 47 - 48: 4.932 distance: 48 - 49: 12.679 distance: 48 - 53: 9.865 distance: 50 - 51: 4.629 distance: 50 - 52: 4.705 distance: 54 - 55: 3.271 distance: 54 - 57: 7.396 distance: 55 - 56: 9.286 distance: 55 - 64: 5.780 distance: 58 - 59: 4.340 distance: 58 - 60: 8.687 distance: 59 - 61: 4.297 distance: 60 - 62: 3.823 distance: 61 - 63: 7.221 distance: 62 - 63: 3.747 distance: 64 - 65: 5.120 distance: 65 - 66: 8.479 distance: 65 - 68: 3.472 distance: 66 - 67: 18.513 distance: 66 - 72: 17.590 distance: 68 - 69: 3.890 distance: 68 - 70: 4.663 distance: 69 - 71: 6.171 distance: 72 - 73: 9.754 distance: 73 - 74: 5.593 distance: 73 - 76: 6.985 distance: 74 - 75: 9.321 distance: 74 - 83: 6.679 distance: 76 - 77: 5.987 distance: 77 - 78: 7.367 distance: 77 - 79: 5.458 distance: 80 - 82: 5.048 distance: 81 - 82: 3.719 distance: 83 - 89: 4.995 distance: 84 - 85: 10.788 distance: 84 - 87: 4.231 distance: 85 - 86: 12.542 distance: 85 - 90: 9.908 distance: 87 - 88: 4.357 distance: 88 - 89: 4.933 distance: 90 - 91: 3.237 distance: 92 - 93: 6.805 distance: 94 - 95: 3.605 distance: 95 - 96: 3.264