Starting phenix.real_space_refine (version: dev) on Sun Dec 18 12:27:51 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/12_2022/6vrl_21370_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/12_2022/6vrl_21370.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/12_2022/6vrl_21370_updated_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/12_2022/6vrl_21370_updated_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/12_2022/6vrl_21370_updated_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/12_2022/6vrl_21370.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/12_2022/6vrl_21370.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/12_2022/6vrl_21370_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/12_2022/6vrl_21370_updated_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.971 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 92 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ASP 393": "OD1" <-> "OD2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A PHE 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "C TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 6141 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4311 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 517} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "B" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 924 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 87 Unusual residues: {'LMT': 1, 'NAG': 2, 'RFY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.05, per 1000 atoms: 0.66 Number of scatterers: 6141 At special positions: 0 Unit cell: (95.256, 104.328, 82.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) I 1 52.95 S 34 16.00 O 1103 8.00 N 958 7.00 C 4045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 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 A 701 " - " ASN A 208 " " NAG A 702 " - " ASN A 217 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.0 seconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 5 sheets defined 46.5% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.740A pdb=" N LEU A 118 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Proline residue: A 120 - end of helix removed outlier: 3.865A pdb=" N PHE A 127 " --> pdb=" O MET A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 143 Processing helix chain 'A' and resid 156 through 189 removed outlier: 3.740A pdb=" N LYS A 159 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLY A 160 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 161 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TYR A 176 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN A 177 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 254 through 269 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.721A pdb=" N LYS A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 299 Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 323 through 337 Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 357 through 389 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 409 through 416 Processing helix chain 'A' and resid 420 through 453 removed outlier: 3.764A pdb=" N ASP A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 4.751A pdb=" N VAL A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N THR A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 495 Processing helix chain 'A' and resid 498 through 513 Processing helix chain 'A' and resid 518 through 529 Processing helix chain 'A' and resid 535 through 542 Processing helix chain 'A' and resid 544 through 558 removed outlier: 3.531A pdb=" N MET A 558 " --> pdb=" O CYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 595 removed outlier: 4.254A pdb=" N SER A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N CYS A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) Proline residue: A 590 - end of helix Processing helix chain 'A' and resid 604 through 610 Processing sheet with id= A, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.525A pdb=" N CYS C 43 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE C 91 " --> pdb=" O CYS C 43 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 105 through 110 removed outlier: 6.006A pdb=" N GLN C 57 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU C 66 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 22 through 25 Processing sheet with id= D, first strand: chain 'B' and resid 37 through 39 removed outlier: 3.811A pdb=" N VAL B 37 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 102 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 39 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET B 100 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 112 through 118 removed outlier: 3.750A pdb=" N VAL B 112 " --> pdb=" O GLN B 58 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET B 53 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE B 70 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LYS B 57 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TRP B 66 " --> pdb=" O LYS B 57 " (cutoff:3.500A) 264 hydrogen bonds defined for protein. 675 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: 1.65 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.40: 2681 1.40 - 1.58: 3595 1.58 - 1.75: 0 1.75 - 1.93: 49 1.93 - 2.11: 1 Bond restraints: 6326 Sorted by residual: bond pdb=" C06 RFY A 704 " pdb=" C07 RFY A 704 " ideal model delta sigma weight residual 1.514 1.576 -0.062 2.00e-02 2.50e+03 9.61e+00 bond pdb=" C04 RFY A 704 " pdb=" N03 RFY A 704 " ideal model delta sigma weight residual 1.445 1.492 -0.047 2.00e-02 2.50e+03 5.50e+00 bond pdb=" C02 RFY A 704 " pdb=" N03 RFY A 704 " ideal model delta sigma weight residual 1.450 1.492 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C05 RFY A 704 " pdb=" C06 RFY A 704 " ideal model delta sigma weight residual 1.531 1.493 0.038 2.00e-02 2.50e+03 3.65e+00 bond pdb=" C01 RFY A 704 " pdb=" C06 RFY A 704 " ideal model delta sigma weight residual 1.526 1.498 0.028 2.00e-02 2.50e+03 2.03e+00 ... (remaining 6321 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.95: 184 106.95 - 113.71: 3435 113.71 - 120.48: 2531 120.48 - 127.24: 2385 127.24 - 134.01: 84 Bond angle restraints: 8619 Sorted by residual: angle pdb=" N VAL A 397 " pdb=" CA VAL A 397 " pdb=" C VAL A 397 " ideal model delta sigma weight residual 113.42 109.33 4.09 1.17e+00 7.31e-01 1.22e+01 angle pdb=" N ARG B 121 " pdb=" CA ARG B 121 " pdb=" C ARG B 121 " ideal model delta sigma weight residual 109.81 117.12 -7.31 2.21e+00 2.05e-01 1.09e+01 angle pdb=" C VAL B 120 " pdb=" N ARG B 121 " pdb=" CA ARG B 121 " ideal model delta sigma weight residual 121.80 128.79 -6.99 2.44e+00 1.68e-01 8.20e+00 angle pdb=" CA VAL A 397 " pdb=" C VAL A 397 " pdb=" N ALA A 398 " ideal model delta sigma weight residual 118.90 116.76 2.14 9.40e-01 1.13e+00 5.20e+00 angle pdb=" C01 RFY A 704 " pdb=" C06 RFY A 704 " pdb=" C05 RFY A 704 " ideal model delta sigma weight residual 107.16 113.59 -6.43 3.00e+00 1.11e-01 4.59e+00 ... (remaining 8614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.02: 3338 22.02 - 44.05: 228 44.05 - 66.07: 20 66.07 - 88.09: 3 88.09 - 110.12: 2 Dihedral angle restraints: 3591 sinusoidal: 1377 harmonic: 2214 Sorted by residual: dihedral pdb=" CA ARG B 121 " pdb=" C ARG B 121 " pdb=" N PRO B 122 " pdb=" CA PRO B 122 " ideal model delta harmonic sigma weight residual 180.00 128.14 51.86 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CB CYS A 200 " pdb=" SG CYS A 200 " pdb=" SG CYS A 209 " pdb=" CB CYS A 209 " ideal model delta sinusoidal sigma weight residual 93.00 133.61 -40.61 1 1.00e+01 1.00e-02 2.31e+01 dihedral pdb=" C01 RFY A 704 " pdb=" C02 RFY A 704 " pdb=" N03 RFY A 704 " pdb=" C04 RFY A 704 " ideal model delta sinusoidal sigma weight residual -53.70 56.42 -110.12 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 3588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 582 0.028 - 0.056: 261 0.056 - 0.084: 85 0.084 - 0.112: 32 0.112 - 0.140: 6 Chirality restraints: 966 Sorted by residual: chirality pdb=" CB ILE A 553 " pdb=" CA ILE A 553 " pdb=" CG1 ILE A 553 " pdb=" CG2 ILE A 553 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILE C 114 " pdb=" N ILE C 114 " pdb=" C ILE C 114 " pdb=" CB ILE C 114 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 chirality pdb=" CA VAL B 91 " pdb=" N VAL B 91 " pdb=" C VAL B 91 " pdb=" CB VAL B 91 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 963 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 121 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO B 122 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 465 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C PHE A 465 " 0.034 2.00e-02 2.50e+03 pdb=" O PHE A 465 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL A 466 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 589 " 0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 590 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 590 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 590 " 0.017 5.00e-02 4.00e+02 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.72: 265 2.72 - 3.28: 6934 3.28 - 3.84: 11086 3.84 - 4.40: 13089 4.40 - 4.96: 22141 Nonbonded interactions: 53515 Sorted by model distance: nonbonded pdb=" OG1 THR C 83 " pdb=" O THR C 94 " model vdw 2.159 2.440 nonbonded pdb=" OG SER B 110 " pdb=" O LEU B 134 " model vdw 2.173 2.440 nonbonded pdb=" O THR A 221 " pdb=" OG SER A 224 " model vdw 2.202 2.440 nonbonded pdb=" O ASP C 102 " pdb=" OH TYR C 106 " model vdw 2.235 2.440 nonbonded pdb=" O SER A 559 " pdb=" O6' LMT A 703 " model vdw 2.267 2.440 ... (remaining 53510 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians I 1 10.91 5 S 34 5.16 5 C 4045 2.51 5 N 958 2.21 5 O 1103 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 13.520 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.050 Process input model: 20.040 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 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 : 0.002 0.062 6326 Z= 0.164 Angle : 0.554 7.308 8619 Z= 0.310 Chirality : 0.037 0.140 966 Planarity : 0.004 0.067 1048 Dihedral : 14.016 110.118 2176 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -3.12 (0.27), residues: 758 helix: -0.96 (0.24), residues: 360 sheet: -3.12 (0.42), residues: 99 loop : -3.02 (0.32), residues: 299 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1683 time to fit residues: 46.0267 Evaluate side-chains 146 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.696 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 6326 Z= 0.199 Angle : 0.633 9.227 8619 Z= 0.315 Chirality : 0.040 0.258 966 Planarity : 0.005 0.071 1048 Dihedral : 5.412 60.614 860 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 2.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -2.02 (0.30), residues: 758 helix: 0.08 (0.27), residues: 354 sheet: -2.86 (0.42), residues: 106 loop : -2.46 (0.35), residues: 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 168 average time/residue: 0.1475 time to fit residues: 33.6681 Evaluate side-chains 154 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 0.584 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0655 time to fit residues: 2.0480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 56 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 0.3980 chunk 73 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6326 Z= 0.168 Angle : 0.601 11.259 8619 Z= 0.297 Chirality : 0.039 0.183 966 Planarity : 0.004 0.071 1048 Dihedral : 4.794 50.875 860 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.61 (0.30), residues: 758 helix: 0.33 (0.28), residues: 352 sheet: -2.51 (0.44), residues: 99 loop : -2.19 (0.35), residues: 307 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 161 average time/residue: 0.1502 time to fit residues: 33.2250 Evaluate side-chains 146 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 141 time to evaluate : 0.662 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0657 time to fit residues: 1.4776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 0.5980 chunk 51 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 6326 Z= 0.386 Angle : 0.760 10.866 8619 Z= 0.386 Chirality : 0.045 0.171 966 Planarity : 0.005 0.075 1048 Dihedral : 5.876 57.328 860 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer Outliers : 4.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -2.02 (0.29), residues: 758 helix: -0.17 (0.26), residues: 354 sheet: -2.89 (0.41), residues: 106 loop : -2.09 (0.36), residues: 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 0.686 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 23 residues processed: 163 average time/residue: 0.1585 time to fit residues: 35.2931 Evaluate side-chains 158 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 0.726 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.0630 time to fit residues: 3.5432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6326 Z= 0.203 Angle : 0.635 10.612 8619 Z= 0.319 Chirality : 0.041 0.150 966 Planarity : 0.004 0.074 1048 Dihedral : 5.327 53.371 860 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer Outliers : 3.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.70 (0.30), residues: 758 helix: 0.02 (0.27), residues: 354 sheet: -2.51 (0.43), residues: 100 loop : -1.95 (0.36), residues: 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 159 average time/residue: 0.1581 time to fit residues: 34.3688 Evaluate side-chains 147 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 0.717 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0629 time to fit residues: 2.3655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 0.0040 chunk 69 optimal weight: 0.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6326 Z= 0.182 Angle : 0.632 11.210 8619 Z= 0.316 Chirality : 0.040 0.169 966 Planarity : 0.004 0.073 1048 Dihedral : 5.160 53.298 860 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.41 (0.30), residues: 758 helix: 0.25 (0.27), residues: 348 sheet: -2.21 (0.45), residues: 99 loop : -1.81 (0.36), residues: 311 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 153 average time/residue: 0.1596 time to fit residues: 33.4171 Evaluate side-chains 148 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 0.690 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0767 time to fit residues: 1.9521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 45 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6326 Z= 0.195 Angle : 0.643 10.715 8619 Z= 0.321 Chirality : 0.041 0.154 966 Planarity : 0.004 0.073 1048 Dihedral : 5.205 53.422 860 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.30), residues: 758 helix: 0.34 (0.27), residues: 349 sheet: -2.17 (0.45), residues: 99 loop : -1.73 (0.36), residues: 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 145 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 149 average time/residue: 0.1483 time to fit residues: 30.7597 Evaluate side-chains 138 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 0.734 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0676 time to fit residues: 1.6722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.7544 > 50: distance: 44 - 67: 4.194 distance: 50 - 76: 8.515 distance: 59 - 85: 19.283 distance: 62 - 67: 3.458 distance: 63 - 93: 21.373 distance: 67 - 68: 4.211 distance: 68 - 69: 4.843 distance: 68 - 71: 4.271 distance: 69 - 70: 9.784 distance: 69 - 76: 7.060 distance: 72 - 73: 4.795 distance: 73 - 74: 4.062 distance: 74 - 75: 7.087 distance: 76 - 77: 9.014 distance: 77 - 78: 10.017 distance: 77 - 80: 11.026 distance: 78 - 79: 29.385 distance: 78 - 85: 9.204 distance: 80 - 81: 10.365 distance: 81 - 82: 4.535 distance: 82 - 83: 9.606 distance: 82 - 84: 4.034 distance: 85 - 86: 23.450 distance: 86 - 87: 11.795 distance: 86 - 89: 9.413 distance: 87 - 88: 29.630 distance: 87 - 93: 12.013 distance: 89 - 90: 13.150 distance: 90 - 91: 6.795 distance: 91 - 92: 5.964 distance: 93 - 94: 27.264 distance: 94 - 95: 23.233 distance: 94 - 97: 12.632 distance: 95 - 96: 13.305 distance: 95 - 101: 25.597 distance: 97 - 98: 18.718 distance: 98 - 99: 24.928 distance: 98 - 100: 21.849 distance: 101 - 102: 18.085 distance: 102 - 103: 23.450 distance: 103 - 104: 28.838 distance: 103 - 105: 13.764 distance: 105 - 106: 20.028 distance: 106 - 107: 10.148 distance: 106 - 109: 15.233 distance: 107 - 108: 17.313 distance: 107 - 116: 48.313 distance: 109 - 110: 14.037 distance: 110 - 111: 7.204 distance: 110 - 112: 7.927 distance: 111 - 113: 8.417 distance: 112 - 114: 10.898 distance: 113 - 115: 8.976 distance: 114 - 115: 11.648 distance: 116 - 117: 37.470 distance: 117 - 118: 14.599 distance: 117 - 120: 32.844 distance: 118 - 119: 17.360 distance: 118 - 122: 17.903 distance: 120 - 121: 32.913 distance: 122 - 123: 13.788 distance: 122 - 128: 3.726 distance: 123 - 124: 13.658 distance: 123 - 126: 15.028 distance: 124 - 125: 15.785 distance: 124 - 129: 15.357 distance: 126 - 127: 7.910 distance: 127 - 128: 19.946 distance: 129 - 130: 11.102 distance: 130 - 131: 23.350 distance: 131 - 132: 21.259 distance: 131 - 133: 11.080 distance: 133 - 134: 15.908 distance: 134 - 135: 9.190 distance: 134 - 137: 8.437 distance: 135 - 136: 11.010 distance: 135 - 147: 21.896 distance: 136 - 175: 30.675 distance: 137 - 138: 13.493 distance: 138 - 139: 11.305 distance: 138 - 140: 8.011 distance: 139 - 141: 5.413 distance: 140 - 142: 24.849 distance: 140 - 143: 8.296 distance: 141 - 142: 15.585 distance: 142 - 144: 8.119 distance: 143 - 145: 5.801 distance: 144 - 146: 6.090 distance: 145 - 146: 5.991