Starting phenix.real_space_refine on Wed Jan 15 02:19:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xh7_38343/01_2025/8xh7_38343.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xh7_38343/01_2025/8xh7_38343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xh7_38343/01_2025/8xh7_38343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xh7_38343/01_2025/8xh7_38343.map" model { file = "/net/cci-nas-00/data/ceres_data/8xh7_38343/01_2025/8xh7_38343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xh7_38343/01_2025/8xh7_38343.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 42 5.16 5 C 5610 2.51 5 N 1134 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7902 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1317 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 1, 'TRANS': 159} Chain: "E" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1317 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 1, 'TRANS': 159} Chain: "F" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1317 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 1, 'TRANS': 159} Chain: "A" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1317 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 1, 'TRANS': 159} Chain: "B" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1317 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 1, 'TRANS': 159} Chain: "D" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1317 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 1, 'TRANS': 159} Time building chain proxies: 4.48, per 1000 atoms: 0.57 Number of scatterers: 7902 At special positions: 0 Unit cell: (125.32, 109.2, 60.32, 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 42 16.00 O 1116 8.00 N 1134 7.00 C 5610 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 - 3.00 Amino acid : True - 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: 1.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 90.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'C' and resid 24 through 45 Processing helix chain 'C' and resid 51 through 72 removed outlier: 3.932A pdb=" N LEU C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 78 through 99 removed outlier: 4.659A pdb=" N ASN C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 134 Processing helix chain 'C' and resid 136 through 160 Processing helix chain 'C' and resid 162 through 180 removed outlier: 3.612A pdb=" N LEU C 168 " --> pdb=" O TRP C 164 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 44 removed outlier: 3.826A pdb=" N MET E 44 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 72 removed outlier: 3.926A pdb=" N VAL E 54 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 98 removed outlier: 3.793A pdb=" N LEU E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 134 removed outlier: 3.636A pdb=" N LEU E 107 " --> pdb=" O GLN E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 160 removed outlier: 3.550A pdb=" N TYR E 159 " --> pdb=" O ILE E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 184 removed outlier: 3.545A pdb=" N LEU E 168 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET E 184 " --> pdb=" O ILE E 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 44 removed outlier: 3.757A pdb=" N MET F 44 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 73 removed outlier: 3.800A pdb=" N VAL F 54 " --> pdb=" O GLY F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 77 removed outlier: 3.898A pdb=" N LEU F 77 " --> pdb=" O ARG F 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 74 through 77' Processing helix chain 'F' and resid 78 through 100 removed outlier: 3.535A pdb=" N GLY F 82 " --> pdb=" O CYS F 78 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN F 99 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 134 Processing helix chain 'F' and resid 136 through 160 Processing helix chain 'F' and resid 162 through 180 Processing helix chain 'A' and resid 25 through 44 removed outlier: 3.852A pdb=" N MET A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 72 removed outlier: 3.926A pdb=" N VAL A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 98 removed outlier: 3.774A pdb=" N LEU A 83 " --> pdb=" O PRO A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 134 removed outlier: 3.665A pdb=" N LEU A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 160 removed outlier: 3.557A pdb=" N TYR A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 184 removed outlier: 3.552A pdb=" N LEU A 168 " --> pdb=" O TRP A 164 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 44 removed outlier: 3.502A pdb=" N MET B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 73 removed outlier: 3.808A pdb=" N VAL B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 77 removed outlier: 3.883A pdb=" N LEU B 77 " --> pdb=" O ARG B 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 74 through 77' Processing helix chain 'B' and resid 78 through 100 removed outlier: 3.540A pdb=" N GLY B 82 " --> pdb=" O CYS B 78 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 134 Processing helix chain 'B' and resid 136 through 160 Processing helix chain 'B' and resid 162 through 180 Processing helix chain 'D' and resid 25 through 45 Processing helix chain 'D' and resid 51 through 72 removed outlier: 3.869A pdb=" N LEU D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 77 Processing helix chain 'D' and resid 78 through 99 removed outlier: 4.645A pdb=" N ASN D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 134 Processing helix chain 'D' and resid 136 through 160 Processing helix chain 'D' and resid 162 through 180 removed outlier: 3.655A pdb=" N LEU D 168 " --> pdb=" O TRP D 164 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE D 180 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 683 hydrogen bonds defined for protein. 2037 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: 2.20 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1044 1.29 - 1.43: 2259 1.43 - 1.57: 4749 1.57 - 1.70: 0 1.70 - 1.84: 72 Bond restraints: 8124 Sorted by residual: bond pdb=" C MET A 61 " pdb=" O MET A 61 " ideal model delta sigma weight residual 1.237 1.157 0.080 1.17e-02 7.31e+03 4.66e+01 bond pdb=" N ILE E 64 " pdb=" CA ILE E 64 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.17e-02 7.31e+03 1.10e+01 bond pdb=" N ILE A 64 " pdb=" CA ILE A 64 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.17e-02 7.31e+03 1.09e+01 bond pdb=" N LEU B 181 " pdb=" CA LEU B 181 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.06e+01 bond pdb=" N ILE D 69 " pdb=" CA ILE D 69 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.04e+01 ... (remaining 8119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 10134 1.46 - 2.91: 754 2.91 - 4.37: 170 4.37 - 5.83: 53 5.83 - 7.29: 13 Bond angle restraints: 11124 Sorted by residual: angle pdb=" CA MET A 61 " pdb=" C MET A 61 " pdb=" O MET A 61 " ideal model delta sigma weight residual 120.55 113.26 7.29 1.06e+00 8.90e-01 4.72e+01 angle pdb=" CA ILE C 180 " pdb=" C ILE C 180 " pdb=" O ILE C 180 " ideal model delta sigma weight residual 122.13 116.43 5.70 1.11e+00 8.12e-01 2.64e+01 angle pdb=" C ALA F 59 " pdb=" N LEU F 60 " pdb=" CA LEU F 60 " ideal model delta sigma weight residual 120.31 113.36 6.95 1.52e+00 4.33e-01 2.09e+01 angle pdb=" O LEU C 60 " pdb=" C LEU C 60 " pdb=" N MET C 61 " ideal model delta sigma weight residual 122.12 126.81 -4.69 1.06e+00 8.90e-01 1.96e+01 angle pdb=" N MET A 61 " pdb=" CA MET A 61 " pdb=" C MET A 61 " ideal model delta sigma weight residual 111.28 106.48 4.80 1.09e+00 8.42e-01 1.94e+01 ... (remaining 11119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 3883 16.11 - 32.22: 436 32.22 - 48.33: 139 48.33 - 64.44: 22 64.44 - 80.55: 2 Dihedral angle restraints: 4482 sinusoidal: 1692 harmonic: 2790 Sorted by residual: dihedral pdb=" C ILE A 71 " pdb=" N ILE A 71 " pdb=" CA ILE A 71 " pdb=" CB ILE A 71 " ideal model delta harmonic sigma weight residual -122.00 -130.43 8.43 0 2.50e+00 1.60e-01 1.14e+01 dihedral pdb=" CA ASP B 75 " pdb=" CB ASP B 75 " pdb=" CG ASP B 75 " pdb=" OD1 ASP B 75 " ideal model delta sinusoidal sigma weight residual -30.00 -86.90 56.90 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASP F 75 " pdb=" CB ASP F 75 " pdb=" CG ASP F 75 " pdb=" OD1 ASP F 75 " ideal model delta sinusoidal sigma weight residual -30.00 -86.88 56.88 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 4479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1180 0.067 - 0.134: 146 0.134 - 0.201: 61 0.201 - 0.268: 28 0.268 - 0.335: 7 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA ILE E 64 " pdb=" N ILE E 64 " pdb=" C ILE E 64 " pdb=" CB ILE E 64 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA ILE A 64 " pdb=" N ILE A 64 " pdb=" C ILE A 64 " pdb=" CB ILE A 64 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA LEU B 88 " pdb=" N LEU B 88 " pdb=" C LEU B 88 " pdb=" CB LEU B 88 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 1419 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 47 " -0.019 2.00e-02 2.50e+03 1.19e-02 3.53e+00 pdb=" CG TRP A 47 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 47 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP A 47 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 47 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 47 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 47 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 47 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 47 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 47 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 153 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C LEU E 153 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU E 153 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU E 154 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 62 " -0.008 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C LEU A 62 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU A 62 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 63 " -0.010 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 2753 2.88 - 3.39: 8491 3.39 - 3.89: 13348 3.89 - 4.40: 14230 4.40 - 4.90: 23282 Nonbonded interactions: 62104 Sorted by model distance: nonbonded pdb=" O TRP C 47 " pdb=" OG1 THR C 48 " model vdw 2.376 3.040 nonbonded pdb=" O TRP D 47 " pdb=" OG1 THR D 48 " model vdw 2.393 3.040 nonbonded pdb=" NH1 ARG F 73 " pdb=" O MET F 184 " model vdw 2.397 3.120 nonbonded pdb=" O LEU F 154 " pdb=" CD1 LEU F 158 " model vdw 2.414 3.460 nonbonded pdb=" O TRP F 47 " pdb=" OG1 THR F 48 " model vdw 2.460 3.040 ... (remaining 62099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.630 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 21.430 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 : 0.005 0.080 8124 Z= 0.345 Angle : 0.913 7.286 11124 Z= 0.631 Chirality : 0.065 0.335 1422 Planarity : 0.003 0.021 1206 Dihedral : 14.929 80.553 2682 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.17 % Allowed : 4.59 % Favored : 93.24 % 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: 2.45 (0.27), residues: 954 helix: 2.03 (0.17), residues: 864 sheet: None (None), residues: 0 loop : -2.55 (0.55), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 47 HIS 0.000 0.000 HIS D 101 PHE 0.018 0.001 PHE D 58 TYR 0.010 0.001 TYR D 41 ARG 0.002 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.768 Fit side-chains REVERT: C 40 LEU cc_start: 0.8526 (tp) cc_final: 0.8214 (tp) REVERT: C 44 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7694 (mpp) REVERT: F 140 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.7018 (mp) REVERT: A 178 MET cc_start: 0.6683 (tpp) cc_final: 0.6433 (mmt) REVERT: B 165 TRP cc_start: 0.7807 (t-100) cc_final: 0.7548 (t-100) outliers start: 18 outliers final: 7 residues processed: 206 average time/residue: 0.1477 time to fit residues: 44.3050 Evaluate side-chains 165 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 158 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 0.0470 chunk 56 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 101 HIS B 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.209073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.180554 restraints weight = 8923.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.181942 restraints weight = 7167.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.182969 restraints weight = 6290.684| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8124 Z= 0.185 Angle : 0.578 10.803 11124 Z= 0.271 Chirality : 0.035 0.161 1422 Planarity : 0.003 0.023 1206 Dihedral : 5.104 47.970 1027 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.05 % Allowed : 16.79 % Favored : 81.16 % 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: 3.22 (0.27), residues: 954 helix: 2.52 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.91 (0.58), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 164 HIS 0.007 0.002 HIS F 101 PHE 0.010 0.001 PHE D 112 TYR 0.010 0.001 TYR C 41 ARG 0.002 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.764 Fit side-chains REVERT: C 44 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7679 (mtp) REVERT: B 165 TRP cc_start: 0.7933 (t-100) cc_final: 0.7415 (t-100) outliers start: 17 outliers final: 8 residues processed: 170 average time/residue: 0.1367 time to fit residues: 35.0847 Evaluate side-chains 156 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 144 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 66 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 101 HIS B 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.216700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.179586 restraints weight = 9726.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.183049 restraints weight = 6663.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.185169 restraints weight = 5275.828| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8124 Z= 0.194 Angle : 0.564 11.119 11124 Z= 0.264 Chirality : 0.034 0.162 1422 Planarity : 0.002 0.023 1206 Dihedral : 4.578 53.671 1013 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.14 % Allowed : 18.36 % Favored : 78.50 % 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: 3.37 (0.27), residues: 954 helix: 2.62 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.82 (0.61), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 131 HIS 0.004 0.001 HIS F 101 PHE 0.009 0.001 PHE E 112 TYR 0.010 0.001 TYR D 41 ARG 0.002 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.852 Fit side-chains REVERT: C 113 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8332 (mp) REVERT: E 131 TRP cc_start: 0.8325 (t-100) cc_final: 0.8063 (t-100) REVERT: F 155 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8550 (mt) REVERT: B 155 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8562 (mt) REVERT: D 113 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8315 (mp) outliers start: 26 outliers final: 17 residues processed: 168 average time/residue: 0.1513 time to fit residues: 37.6914 Evaluate side-chains 170 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 164 TRP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 164 TRP Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 144 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 1 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.214887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.176755 restraints weight = 9707.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.180130 restraints weight = 6630.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.182252 restraints weight = 5280.799| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8124 Z= 0.193 Angle : 0.567 10.687 11124 Z= 0.262 Chirality : 0.034 0.166 1422 Planarity : 0.002 0.023 1206 Dihedral : 4.614 53.603 1013 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.74 % Allowed : 21.26 % Favored : 75.00 % 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: 3.48 (0.27), residues: 954 helix: 2.68 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.66 (0.65), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 164 HIS 0.001 0.000 HIS D 101 PHE 0.009 0.001 PHE E 112 TYR 0.009 0.001 TYR D 41 ARG 0.001 0.000 ARG F 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.782 Fit side-chains REVERT: C 113 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8351 (mp) REVERT: F 113 ILE cc_start: 0.8147 (tp) cc_final: 0.7630 (pt) REVERT: F 155 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8545 (mt) REVERT: B 113 ILE cc_start: 0.8169 (tp) cc_final: 0.7704 (pt) REVERT: B 155 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8556 (mt) REVERT: D 113 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8308 (mp) outliers start: 31 outliers final: 19 residues processed: 169 average time/residue: 0.1488 time to fit residues: 37.2551 Evaluate side-chains 173 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 164 TRP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 98 TRP Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 164 TRP Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 144 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 90 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 101 HIS B 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.204628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.174154 restraints weight = 9021.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.175528 restraints weight = 7195.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.176796 restraints weight = 6311.975| |-----------------------------------------------------------------------------| r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8124 Z= 0.192 Angle : 0.559 10.330 11124 Z= 0.261 Chirality : 0.034 0.174 1422 Planarity : 0.002 0.022 1206 Dihedral : 4.603 54.747 1013 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.47 % Allowed : 21.38 % Favored : 74.15 % 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: 3.51 (0.27), residues: 954 helix: 2.69 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.60 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 131 HIS 0.005 0.001 HIS F 101 PHE 0.009 0.001 PHE E 112 TYR 0.010 0.001 TYR D 41 ARG 0.002 0.000 ARG F 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.759 Fit side-chains REVERT: C 113 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8486 (mp) REVERT: F 113 ILE cc_start: 0.8117 (tp) cc_final: 0.7690 (pt) REVERT: F 155 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8711 (mt) REVERT: B 113 ILE cc_start: 0.8141 (tp) cc_final: 0.7729 (pt) REVERT: B 155 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8709 (mt) REVERT: D 44 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7233 (mpp) REVERT: D 113 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8461 (mp) outliers start: 37 outliers final: 23 residues processed: 173 average time/residue: 0.1517 time to fit residues: 39.4273 Evaluate side-chains 180 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 164 TRP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 164 TRP Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 144 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.6864 > 50: distance: 38 - 42: 27.476 distance: 42 - 43: 33.891 distance: 43 - 44: 33.807 distance: 43 - 46: 26.371 distance: 44 - 45: 15.136 distance: 44 - 53: 36.712 distance: 45 - 72: 30.059 distance: 46 - 47: 18.091 distance: 47 - 48: 9.208 distance: 48 - 49: 5.913 distance: 49 - 50: 14.322 distance: 50 - 51: 11.721 distance: 50 - 52: 8.357 distance: 53 - 54: 16.485 distance: 54 - 55: 20.628 distance: 54 - 57: 6.435 distance: 55 - 56: 26.617 distance: 55 - 64: 11.746 distance: 56 - 80: 21.240 distance: 57 - 58: 10.055 distance: 58 - 59: 9.002 distance: 59 - 60: 6.955 distance: 60 - 61: 8.450 distance: 61 - 62: 8.845 distance: 61 - 63: 7.686 distance: 64 - 65: 14.652 distance: 65 - 66: 17.363 distance: 65 - 68: 21.073 distance: 66 - 67: 27.998 distance: 66 - 72: 17.743 distance: 68 - 69: 12.008 distance: 69 - 70: 18.382 distance: 69 - 71: 12.778 distance: 72 - 73: 40.785 distance: 73 - 74: 45.926 distance: 73 - 76: 29.926 distance: 74 - 75: 34.308 distance: 74 - 80: 16.566 distance: 76 - 77: 17.469 distance: 77 - 78: 33.348 distance: 77 - 79: 18.363 distance: 80 - 81: 18.679 distance: 81 - 82: 9.746 distance: 81 - 84: 35.990 distance: 82 - 83: 22.945 distance: 82 - 88: 38.873 distance: 84 - 85: 27.833 distance: 85 - 86: 61.686 distance: 85 - 87: 47.828 distance: 88 - 89: 42.749 distance: 89 - 90: 31.645 distance: 89 - 92: 6.887 distance: 90 - 91: 23.446 distance: 90 - 94: 16.795 distance: 91 - 113: 51.149 distance: 92 - 93: 40.029 distance: 94 - 95: 8.574 distance: 94 - 100: 9.625 distance: 95 - 96: 3.718 distance: 95 - 98: 28.447 distance: 96 - 97: 35.728 distance: 96 - 101: 14.522 distance: 97 - 117: 20.775 distance: 98 - 99: 59.251 distance: 99 - 100: 29.427 distance: 101 - 102: 19.297 distance: 102 - 103: 10.893 distance: 102 - 105: 21.239 distance: 103 - 104: 24.182 distance: 103 - 109: 12.669 distance: 104 - 124: 22.930 distance: 105 - 106: 20.314 distance: 106 - 107: 14.237 distance: 106 - 108: 11.616 distance: 109 - 110: 42.234 distance: 110 - 111: 28.025 distance: 111 - 112: 29.265 distance: 111 - 113: 31.393 distance: 112 - 127: 20.629 distance: 113 - 114: 45.432 distance: 114 - 115: 15.028 distance: 115 - 116: 48.547 distance: 115 - 117: 28.262 distance: 116 - 135: 22.314