Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 03:31:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woc_32648/04_2023/7woc_32648.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woc_32648/04_2023/7woc_32648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woc_32648/04_2023/7woc_32648.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woc_32648/04_2023/7woc_32648.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woc_32648/04_2023/7woc_32648.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woc_32648/04_2023/7woc_32648.pdb" } resolution = 3.35 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= 0.000 sd= 0.001 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 18 5.16 5 C 3012 2.51 5 N 804 2.21 5 O 912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ARG 98": "NH1" <-> "NH2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 4746 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "A" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1560 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 12, 'TRANS': 191} Chain breaks: 2 Chain: "B" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1636 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 199} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" 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 chiralities: 1 Time building chain proxies: 2.84, per 1000 atoms: 0.60 Number of scatterers: 4746 At special positions: 0 Unit cell: (91.02, 68.06, 119.72, 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 18 16.00 O 912 8.00 N 804 7.00 C 3012 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 203 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 195 " 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 C 601 " - " ASN C 343 " Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 742.7 milliseconds 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1132 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 14 sheets defined 6.1% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.904A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.612A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 390' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.836A pdb=" N ASP A 90 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 91' Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.749A pdb=" N LYS B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.766A pdb=" N LYS B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 185 through 190' Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.543A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.663A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.724A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 5 through 6 removed outlier: 3.568A pdb=" N VAL A 20 " --> pdb=" O MET A 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 57 through 60 removed outlier: 3.604A pdb=" N ILE A 57 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 92 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 116 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.835A pdb=" N LEU A 148 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 145 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 185 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A 188 " --> pdb=" O HIS A 171 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N HIS A 171 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 157 through 159 removed outlier: 3.722A pdb=" N LYS A 216 " --> pdb=" O CYS A 203 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 5 through 6 removed outlier: 4.340A pdb=" N THR B 5 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 24 " --> pdb=" O THR B 5 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AB2, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.726A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR B 98 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AB4, first strand: chain 'B' and resid 117 through 119 removed outlier: 3.742A pdb=" N PHE B 117 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 136 " --> pdb=" O PHE B 117 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 134 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ASN B 138 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU B 176 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 147 through 149 88 hydrogen bonds defined for protein. 228 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: 1.23 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1519 1.34 - 1.46: 1179 1.46 - 1.58: 2147 1.58 - 1.70: 0 1.70 - 1.81: 20 Bond restraints: 4865 Sorted by residual: bond pdb=" C PHE A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 1.331 1.357 -0.026 1.20e-02 6.94e+03 4.78e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C5 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" C GLU A 155 " pdb=" N PRO A 156 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.04e+00 bond pdb=" C3 NAG C 601 " pdb=" O3 NAG C 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.02e+00 ... (remaining 4860 not shown) Histogram of bond angle deviations from ideal: 100.72 - 107.37: 186 107.37 - 114.02: 2673 114.02 - 120.66: 1779 120.66 - 127.31: 1927 127.31 - 133.96: 52 Bond angle restraints: 6617 Sorted by residual: angle pdb=" C VAL B 151 " pdb=" N ASP B 152 " pdb=" CA ASP B 152 " ideal model delta sigma weight residual 121.54 126.42 -4.88 1.91e+00 2.74e-01 6.52e+00 angle pdb=" C PRO A 154 " pdb=" N GLU A 155 " pdb=" CA GLU A 155 " ideal model delta sigma weight residual 120.26 123.62 -3.36 1.34e+00 5.57e-01 6.28e+00 angle pdb=" N ASP B 152 " pdb=" CA ASP B 152 " pdb=" C ASP B 152 " ideal model delta sigma weight residual 110.80 115.23 -4.43 2.13e+00 2.20e-01 4.32e+00 angle pdb=" N GLY B 69 " pdb=" CA GLY B 69 " pdb=" C GLY B 69 " ideal model delta sigma weight residual 113.18 117.74 -4.56 2.37e+00 1.78e-01 3.70e+00 angle pdb=" CA LYS A 208 " pdb=" C LYS A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 118.44 121.34 -2.90 1.59e+00 3.96e-01 3.33e+00 ... (remaining 6612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 2764 17.48 - 34.96: 101 34.96 - 52.44: 13 52.44 - 69.91: 9 69.91 - 87.39: 3 Dihedral angle restraints: 2890 sinusoidal: 1121 harmonic: 1769 Sorted by residual: dihedral pdb=" CA VAL B 151 " pdb=" C VAL B 151 " pdb=" N ASP B 152 " pdb=" CA ASP B 152 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA CYS C 379 " pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " ideal model delta sinusoidal sigma weight residual 79.00 11.66 67.34 1 2.00e+01 2.50e-03 1.48e+01 dihedral pdb=" SG CYS C 391 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " pdb=" CA CYS C 525 " ideal model delta sinusoidal sigma weight residual -73.00 -16.98 -56.02 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 2887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 400 0.025 - 0.050: 198 0.050 - 0.076: 58 0.076 - 0.101: 54 0.101 - 0.126: 19 Chirality restraints: 729 Sorted by residual: chirality pdb=" CA ILE B 59 " pdb=" N ILE B 59 " pdb=" C ILE B 59 " pdb=" CB ILE B 59 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA VAL A 157 " pdb=" N VAL A 157 " pdb=" C VAL A 157 " pdb=" CB VAL A 157 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA ILE C 434 " pdb=" N ILE C 434 " pdb=" C ILE C 434 " pdb=" CB ILE C 434 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.36e-01 ... (remaining 726 not shown) Planarity restraints: 856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO C 521 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 40 " 0.030 5.00e-02 4.00e+02 4.65e-02 3.45e+00 pdb=" N PRO A 41 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 14 " 0.019 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO B 15 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 15 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 15 " 0.016 5.00e-02 4.00e+02 ... (remaining 853 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1314 2.81 - 3.33: 4052 3.33 - 3.86: 7727 3.86 - 4.38: 8853 4.38 - 4.90: 15570 Nonbonded interactions: 37516 Sorted by model distance: nonbonded pdb=" O GLU B 124 " pdb=" OG SER B 128 " model vdw 2.288 2.440 nonbonded pdb=" OG1 THR A 69 " pdb=" OE1 GLU A 82 " model vdw 2.320 2.440 nonbonded pdb=" OD1 ASN A 206 " pdb=" NZ LYS A 213 " model vdw 2.342 2.520 nonbonded pdb=" OD1 ASN C 448 " pdb=" ND2 ASN C 450 " model vdw 2.348 2.520 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.352 2.440 ... (remaining 37511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.360 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 16.280 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 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 0.041 4865 Z= 0.122 Angle : 0.477 5.523 6617 Z= 0.256 Chirality : 0.041 0.126 729 Planarity : 0.004 0.047 855 Dihedral : 9.560 87.392 1734 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer Outliers : 4.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (0.27), residues: 600 helix: -4.88 (0.19), residues: 36 sheet: -2.38 (0.36), residues: 175 loop : -3.63 (0.24), residues: 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 7 residues processed: 189 average time/residue: 0.2217 time to fit residues: 50.0153 Evaluate side-chains 106 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.574 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0520 time to fit residues: 1.4226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 0.0270 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 439 ASN C 493 GLN A 1 GLN A 178 GLN B 30 ASN B 125 GLN B 148 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4041 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: