Starting phenix.real_space_refine (version: dev) on Mon Feb 20 09:56:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlr_32591/02_2023/7wlr_32591.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlr_32591/02_2023/7wlr_32591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlr_32591/02_2023/7wlr_32591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlr_32591/02_2023/7wlr_32591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlr_32591/02_2023/7wlr_32591.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlr_32591/02_2023/7wlr_32591.pdb" } resolution = 3.54 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= 1.000 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 Process input model Symmetric amino acids flipped Residue "A GLU 51": "OE1" <-> "OE2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E GLU 74": "OE1" <-> "OE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E GLU 106": "OE1" <-> "OE2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H GLU 39": "OE1" <-> "OE2" Residue "H GLU 75": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11922 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 794 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "B" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 666 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 802 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 740 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 794 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 813 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 714 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 6.90, per 1000 atoms: 0.58 Number of scatterers: 11922 At special positions: 0 Unit cell: (118.72, 86.92, 119.78, 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) S 6 16.00 P 289 15.00 O 2817 8.00 N 2222 7.00 C 6588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.28 Conformation dependent library (CDL) restraints added in 1.1 seconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 74.5% alpha, 3.2% beta 144 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 5.49 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 80 removed outlier: 4.142A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 removed outlier: 3.688A pdb=" N ALA A 115 " --> pdb=" O CYS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.755A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.815A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.439A pdb=" N VAL C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 41 through 53 removed outlier: 3.925A pdb=" N LYS D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 88 removed outlier: 3.510A pdb=" N ASN D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 106 Processing helix chain 'D' and resid 107 through 129 Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 64 through 78 removed outlier: 3.880A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 removed outlier: 3.642A pdb=" N ALA E 115 " --> pdb=" O CYS E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 132 removed outlier: 3.507A pdb=" N ILE E 125 " --> pdb=" O GLN E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.999A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.426A pdb=" N VAL G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 41 through 53 Processing helix chain 'H' and resid 59 through 88 Processing helix chain 'H' and resid 94 through 106 Processing helix chain 'H' and resid 107 through 129 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.306A pdb=" N ARG A 84 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.520A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.377A pdb=" N ARG C 42 " --> pdb=" O ILE D 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 7.067A pdb=" N ARG E 84 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.113A pdb=" N ARG G 42 " --> pdb=" O ILE H 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 418 hydrogen bonds defined for protein. 1233 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 4.39 Time building geometry restraints manager: 6.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1476 1.32 - 1.44: 4699 1.44 - 1.56: 5959 1.56 - 1.69: 577 1.69 - 1.81: 10 Bond restraints: 12721 Sorted by residual: bond pdb=" N ARG B 23 " pdb=" CA ARG B 23 " ideal model delta sigma weight residual 1.457 1.511 -0.054 1.29e-02 6.01e+03 1.75e+01 bond pdb=" C ARG B 35 " pdb=" O ARG B 35 " ideal model delta sigma weight residual 1.237 1.197 0.040 1.19e-02 7.06e+03 1.14e+01 bond pdb=" CZ ARG C 32 " pdb=" NH2 ARG C 32 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.07e+01 bond pdb=" CZ ARG F 35 " pdb=" NH2 ARG F 35 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.02e+01 bond pdb=" CZ ARG A 135 " pdb=" NH2 ARG A 135 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.02e+01 ... (remaining 12716 not shown) Histogram of bond angle deviations from ideal: 97.95 - 104.87: 1184 104.87 - 111.79: 6702 111.79 - 118.72: 3436 118.72 - 125.64: 6104 125.64 - 132.56: 998 Bond angle restraints: 18424 Sorted by residual: angle pdb=" C THR A 59 " pdb=" N GLU A 60 " pdb=" CA GLU A 60 " ideal model delta sigma weight residual 120.82 127.74 -6.92 1.47e+00 4.63e-01 2.22e+01 angle pdb=" C SER G 14 " pdb=" N THR G 15 " pdb=" CA THR G 15 " ideal model delta sigma weight residual 120.90 127.52 -6.62 1.41e+00 5.03e-01 2.21e+01 angle pdb=" N ARG F 23 " pdb=" CA ARG F 23 " pdb=" C ARG F 23 " ideal model delta sigma weight residual 111.34 118.15 -6.81 1.49e+00 4.50e-01 2.09e+01 angle pdb=" N GLU G 91 " pdb=" CA GLU G 91 " pdb=" C GLU G 91 " ideal model delta sigma weight residual 111.28 115.95 -4.67 1.09e+00 8.42e-01 1.84e+01 angle pdb=" O GLY D 108 " pdb=" C GLY D 108 " pdb=" N GLU D 109 " ideal model delta sigma weight residual 122.13 118.01 4.12 9.90e-01 1.02e+00 1.74e+01 ... (remaining 18419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.23: 4389 21.23 - 42.46: 1134 42.46 - 63.69: 1078 63.69 - 84.92: 46 84.92 - 106.15: 8 Dihedral angle restraints: 6655 sinusoidal: 4461 harmonic: 2194 Sorted by residual: dihedral pdb=" CA GLY E 45 " pdb=" C GLY E 45 " pdb=" N THR E 46 " pdb=" CA THR E 46 " ideal model delta harmonic sigma weight residual 180.00 -154.28 -25.72 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA GLY A 45 " pdb=" C GLY A 45 " pdb=" N THR A 46 " pdb=" CA THR A 46 " ideal model delta harmonic sigma weight residual 180.00 -154.53 -25.47 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ARG B 23 " pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta harmonic sigma weight residual 180.00 -156.82 -23.18 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 6652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1787 0.062 - 0.124: 281 0.124 - 0.187: 25 0.187 - 0.249: 10 0.249 - 0.311: 4 Chirality restraints: 2107 Sorted by residual: chirality pdb=" CA ARG F 23 " pdb=" N ARG F 23 " pdb=" C ARG F 23 " pdb=" CB ARG F 23 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA LYS G 118 " pdb=" N LYS G 118 " pdb=" C LYS G 118 " pdb=" CB LYS G 118 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA THR A 46 " pdb=" N THR A 46 " pdb=" C THR A 46 " pdb=" CB THR A 46 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 2104 not shown) Planarity restraints: 1323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 44 " 0.045 2.00e-02 2.50e+03 3.82e-02 2.92e+01 pdb=" CG TYR D 44 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR D 44 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR D 44 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR D 44 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR D 44 " -0.049 2.00e-02 2.50e+03 pdb=" CZ TYR D 44 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR D 44 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 101 " -0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C GLY B 101 " 0.070 2.00e-02 2.50e+03 pdb=" O GLY B 101 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY B 102 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 53 " 0.014 2.00e-02 2.50e+03 3.24e-02 1.57e+01 pdb=" CG HIS H 53 " -0.005 2.00e-02 2.50e+03 pdb=" ND1 HIS H 53 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS H 53 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 HIS H 53 " -0.035 2.00e-02 2.50e+03 pdb=" NE2 HIS H 53 " 0.055 2.00e-02 2.50e+03 ... (remaining 1320 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1741 2.77 - 3.30: 10480 3.30 - 3.83: 23372 3.83 - 4.37: 27505 4.37 - 4.90: 39362 Nonbonded interactions: 102460 Sorted by model distance: nonbonded pdb=" O2 DC I 50 " pdb=" N2 DG J 96 " model vdw 2.232 2.496 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 72 " model vdw 2.287 2.440 nonbonded pdb=" OG SER H 94 " pdb=" OE1 GLU H 97 " model vdw 2.346 2.440 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.365 2.440 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.383 2.440 ... (remaining 102455 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 118) } ncs_group { reference = (chain 'D' and resid 38 through 129) selection = chain 'H' } 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 P 289 5.49 5 S 6 5.16 5 C 6588 2.51 5 N 2222 2.21 5 O 2817 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 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: 2.320 Check model and map are aligned: 0.210 Process input model: 39.640 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 12721 Z= 0.363 Angle : 0.884 7.744 18424 Z= 0.569 Chirality : 0.049 0.311 2107 Planarity : 0.010 0.124 1323 Dihedral : 29.424 106.152 5235 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.29), residues: 738 helix: 1.78 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -0.77 (0.40), residues: 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.966 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3827 time to fit residues: 51.5755 Evaluate side-chains 58 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: