Starting phenix.real_space_refine on Mon Jun 24 14:31:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctk_26993/06_2024/8ctk_26993.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctk_26993/06_2024/8ctk_26993.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctk_26993/06_2024/8ctk_26993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctk_26993/06_2024/8ctk_26993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctk_26993/06_2024/8ctk_26993.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctk_26993/06_2024/8ctk_26993.pdb" } 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= 0.000 sd= 0.018 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 14 5.16 5 C 2020 2.51 5 N 520 2.21 5 O 488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 18": "OE1" <-> "OE2" Residue "B GLU 18": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 3042 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1521 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain: "B" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1521 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Time building chain proxies: 2.83, per 1000 atoms: 0.93 Number of scatterers: 3042 At special positions: 0 Unit cell: (74.881, 54.525, 80.697, 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 14 16.00 O 488 8.00 N 520 7.00 C 2020 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: 0.96 Conformation dependent library (CDL) restraints added in 680.2 milliseconds 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 700 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 2 sheets defined 48.7% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 17 through 38 removed outlier: 3.836A pdb=" N ASN A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 35 " --> pdb=" O TRP A 31 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 56 through 71 removed outlier: 4.123A pdb=" N TYR A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 107 removed outlier: 3.853A pdb=" N GLY A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.733A pdb=" N ASN A 113 " --> pdb=" O TRP A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 38 removed outlier: 3.622A pdb=" N LEU B 35 " --> pdb=" O TRP B 31 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN B 36 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE B 37 " --> pdb=" O CYS B 33 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 56 through 71 removed outlier: 4.123A pdb=" N TYR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 107 removed outlier: 3.852A pdb=" N GLY B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.732A pdb=" N ASN B 113 " --> pdb=" O TRP B 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 132 removed outlier: 7.079A pdb=" N GLU A 167 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU A 176 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE A 201 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR A 178 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ALA A 195 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N SER A 184 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE A 193 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 149 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 128 through 132 removed outlier: 7.079A pdb=" N GLU B 167 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU B 176 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE B 201 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR B 178 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ALA B 195 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N SER B 184 " --> pdb=" O PHE B 193 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE B 193 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU B 149 " --> pdb=" O LEU B 156 " (cutoff:3.500A) 186 hydrogen bonds defined for protein. 522 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: 0.79 Time building geometry restraints manager: 1.09 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: 924 1.34 - 1.46: 773 1.46 - 1.58: 1409 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 3126 Sorted by residual: bond pdb=" CB ASP B 190 " pdb=" CG ASP B 190 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.08e+00 bond pdb=" CB ASP A 190 " pdb=" CG ASP A 190 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.07e+00 bond pdb=" C TRP A 58 " pdb=" N PRO A 59 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.28e-02 6.10e+03 7.29e-01 bond pdb=" C TRP B 58 " pdb=" N PRO B 59 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.28e-02 6.10e+03 6.67e-01 bond pdb=" CB ASP A 160 " pdb=" CG ASP A 160 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.36e-01 ... (remaining 3121 not shown) Histogram of bond angle deviations from ideal: 99.44 - 106.34: 66 106.34 - 113.25: 1679 113.25 - 120.15: 1102 120.15 - 127.05: 1361 127.05 - 133.95: 46 Bond angle restraints: 4254 Sorted by residual: angle pdb=" N ILE B 73 " pdb=" CA ILE B 73 " pdb=" C ILE B 73 " ideal model delta sigma weight residual 111.62 107.80 3.82 7.90e-01 1.60e+00 2.34e+01 angle pdb=" N ILE A 73 " pdb=" CA ILE A 73 " pdb=" C ILE A 73 " ideal model delta sigma weight residual 111.62 107.82 3.80 7.90e-01 1.60e+00 2.31e+01 angle pdb=" CA MET B 91 " pdb=" CB MET B 91 " pdb=" CG MET B 91 " ideal model delta sigma weight residual 114.10 119.39 -5.29 2.00e+00 2.50e-01 7.00e+00 angle pdb=" CA MET A 91 " pdb=" CB MET A 91 " pdb=" CG MET A 91 " ideal model delta sigma weight residual 114.10 119.35 -5.25 2.00e+00 2.50e-01 6.90e+00 angle pdb=" CA LEU A 56 " pdb=" CB LEU A 56 " pdb=" CG LEU A 56 " ideal model delta sigma weight residual 116.30 124.34 -8.04 3.50e+00 8.16e-02 5.28e+00 ... (remaining 4249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.01: 1512 13.01 - 26.02: 170 26.02 - 39.03: 78 39.03 - 52.03: 22 52.03 - 65.04: 6 Dihedral angle restraints: 1788 sinusoidal: 696 harmonic: 1092 Sorted by residual: dihedral pdb=" CG ARG A 198 " pdb=" CD ARG A 198 " pdb=" NE ARG A 198 " pdb=" CZ ARG A 198 " ideal model delta sinusoidal sigma weight residual 180.00 135.44 44.56 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG B 198 " pdb=" CD ARG B 198 " pdb=" NE ARG B 198 " pdb=" CZ ARG B 198 " ideal model delta sinusoidal sigma weight residual 180.00 135.49 44.51 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" N MET A 84 " pdb=" CA MET A 84 " pdb=" CB MET A 84 " pdb=" CG MET A 84 " ideal model delta sinusoidal sigma weight residual -60.00 -113.00 53.00 3 1.50e+01 4.44e-03 9.17e+00 ... (remaining 1785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 354 0.045 - 0.090: 99 0.090 - 0.134: 30 0.134 - 0.179: 1 0.179 - 0.224: 2 Chirality restraints: 486 Sorted by residual: chirality pdb=" CA ILE A 118 " pdb=" N ILE A 118 " pdb=" C ILE A 118 " pdb=" CB ILE A 118 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE B 118 " pdb=" N ILE B 118 " pdb=" C ILE B 118 " pdb=" CB ILE B 118 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA VAL A 143 " pdb=" N VAL A 143 " pdb=" C VAL A 143 " pdb=" CB VAL A 143 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 483 not shown) Planarity restraints: 512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 31 " 0.025 2.00e-02 2.50e+03 1.49e-02 5.55e+00 pdb=" CG TRP A 31 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 31 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 31 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 31 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 31 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 31 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 31 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 31 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 31 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 31 " -0.025 2.00e-02 2.50e+03 1.48e-02 5.44e+00 pdb=" CG TRP B 31 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP B 31 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 31 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 31 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 31 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 31 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 31 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 31 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 31 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 193 " -0.012 2.00e-02 2.50e+03 1.35e-02 3.19e+00 pdb=" CG PHE A 193 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 193 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 193 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 193 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 193 " -0.015 2.00e-02 2.50e+03 pdb=" CZ PHE A 193 " 0.005 2.00e-02 2.50e+03 ... (remaining 509 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1035 2.86 - 3.37: 2693 3.37 - 3.88: 4899 3.88 - 4.39: 5175 4.39 - 4.90: 8964 Nonbonded interactions: 22766 Sorted by model distance: nonbonded pdb=" O PRO A 132 " pdb=" NE2 HIS A 154 " model vdw 2.347 2.520 nonbonded pdb=" O PRO B 132 " pdb=" NE2 HIS B 154 " model vdw 2.348 2.520 nonbonded pdb=" O VAL A 187 " pdb=" OG SER A 191 " model vdw 2.395 2.440 nonbonded pdb=" O VAL B 187 " pdb=" OG SER B 191 " model vdw 2.395 2.440 nonbonded pdb=" N GLU B 137 " pdb=" OE1 GLU B 137 " model vdw 2.407 2.520 ... (remaining 22761 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 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 4.870 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.730 Find NCS groups from input model: 0.150 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 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 : 0.003 0.035 3126 Z= 0.214 Angle : 0.691 8.040 4254 Z= 0.364 Chirality : 0.047 0.224 486 Planarity : 0.005 0.043 512 Dihedral : 14.365 65.043 1088 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 20.25 % Favored : 79.75 % 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: -1.07 (0.43), residues: 372 helix: 0.55 (0.41), residues: 164 sheet: -0.63 (0.60), residues: 78 loop : -2.38 (0.48), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 31 HIS 0.001 0.000 HIS B 125 PHE 0.027 0.002 PHE A 193 TYR 0.007 0.001 TYR A 47 ARG 0.003 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.329 Fit side-chains REVERT: A 166 LYS cc_start: 0.7853 (tptp) cc_final: 0.7258 (mmpt) REVERT: B 166 LYS cc_start: 0.7666 (tptp) cc_final: 0.7067 (mmpt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1077 time to fit residues: 7.4480 Evaluate side-chains 49 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3126 Z= 0.224 Angle : 0.543 6.849 4254 Z= 0.279 Chirality : 0.043 0.182 486 Planarity : 0.004 0.035 512 Dihedral : 3.640 11.732 420 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.90 % Allowed : 20.89 % Favored : 77.22 % 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: -0.89 (0.43), residues: 372 helix: 0.89 (0.41), residues: 166 sheet: -0.92 (0.58), residues: 78 loop : -2.34 (0.49), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 31 HIS 0.002 0.001 HIS B 125 PHE 0.017 0.002 PHE B 193 TYR 0.008 0.001 TYR A 179 ARG 0.002 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 166 LYS cc_start: 0.7767 (tptp) cc_final: 0.7224 (mmpt) REVERT: B 77 THR cc_start: 0.7584 (p) cc_final: 0.7271 (t) REVERT: B 166 LYS cc_start: 0.7686 (tptp) cc_final: 0.7101 (mmpt) outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 0.1086 time to fit residues: 7.6442 Evaluate side-chains 53 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3126 Z= 0.199 Angle : 0.519 5.938 4254 Z= 0.266 Chirality : 0.042 0.179 486 Planarity : 0.004 0.033 512 Dihedral : 3.576 11.587 420 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.85 % Allowed : 20.57 % Favored : 76.58 % 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: -0.82 (0.43), residues: 372 helix: 1.04 (0.40), residues: 166 sheet: -0.99 (0.58), residues: 78 loop : -2.37 (0.48), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 58 HIS 0.001 0.001 HIS A 154 PHE 0.013 0.002 PHE A 193 TYR 0.008 0.001 TYR A 95 ARG 0.001 0.000 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 77 THR cc_start: 0.7773 (p) cc_final: 0.7505 (t) REVERT: A 166 LYS cc_start: 0.7800 (tptp) cc_final: 0.7265 (mmpt) REVERT: B 166 LYS cc_start: 0.7719 (tptp) cc_final: 0.7196 (mmpt) outliers start: 9 outliers final: 6 residues processed: 58 average time/residue: 0.1040 time to fit residues: 7.9527 Evaluate side-chains 59 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 9 optimal weight: 0.0040 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3126 Z= 0.173 Angle : 0.505 6.713 4254 Z= 0.258 Chirality : 0.042 0.183 486 Planarity : 0.004 0.030 512 Dihedral : 3.494 10.162 420 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.11 % Allowed : 19.30 % Favored : 76.58 % 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: -0.67 (0.43), residues: 372 helix: 1.16 (0.40), residues: 166 sheet: -0.96 (0.59), residues: 78 loop : -2.27 (0.48), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 58 HIS 0.001 0.001 HIS A 154 PHE 0.011 0.001 PHE B 53 TYR 0.007 0.001 TYR B 95 ARG 0.001 0.000 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 77 THR cc_start: 0.7822 (p) cc_final: 0.7588 (t) REVERT: A 166 LYS cc_start: 0.7778 (tptp) cc_final: 0.7266 (mmpt) REVERT: B 77 THR cc_start: 0.7704 (p) cc_final: 0.7421 (t) REVERT: B 166 LYS cc_start: 0.7667 (tptp) cc_final: 0.7156 (mmpt) outliers start: 13 outliers final: 8 residues processed: 64 average time/residue: 0.0995 time to fit residues: 8.4271 Evaluate side-chains 63 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3126 Z= 0.244 Angle : 0.566 6.916 4254 Z= 0.281 Chirality : 0.043 0.182 486 Planarity : 0.004 0.025 512 Dihedral : 3.551 9.448 420 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.06 % Allowed : 18.67 % Favored : 76.27 % 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: -0.65 (0.43), residues: 372 helix: 1.30 (0.40), residues: 166 sheet: -1.11 (0.58), residues: 78 loop : -2.32 (0.47), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 31 HIS 0.002 0.001 HIS A 154 PHE 0.013 0.002 PHE A 193 TYR 0.010 0.001 TYR B 95 ARG 0.001 0.000 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 54 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 166 LYS cc_start: 0.7816 (tptp) cc_final: 0.7306 (mmpt) REVERT: B 166 LYS cc_start: 0.7717 (tptp) cc_final: 0.7246 (mmpt) outliers start: 16 outliers final: 10 residues processed: 62 average time/residue: 0.1036 time to fit residues: 8.4273 Evaluate side-chains 63 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 120 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3126 Z= 0.228 Angle : 0.549 6.777 4254 Z= 0.274 Chirality : 0.043 0.179 486 Planarity : 0.004 0.024 512 Dihedral : 3.549 10.428 420 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.11 % Allowed : 20.25 % Favored : 75.63 % 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: -0.59 (0.43), residues: 372 helix: 1.41 (0.41), residues: 166 sheet: -1.14 (0.58), residues: 78 loop : -2.33 (0.47), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 58 HIS 0.002 0.001 HIS A 154 PHE 0.016 0.002 PHE B 193 TYR 0.008 0.001 TYR A 95 ARG 0.001 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 77 THR cc_start: 0.7833 (p) cc_final: 0.7570 (t) REVERT: A 166 LYS cc_start: 0.7806 (tptp) cc_final: 0.7334 (mmpt) REVERT: B 166 LYS cc_start: 0.7762 (tptp) cc_final: 0.7294 (mmpt) outliers start: 13 outliers final: 10 residues processed: 59 average time/residue: 0.1072 time to fit residues: 8.3591 Evaluate side-chains 65 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 120 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3126 Z= 0.254 Angle : 0.576 6.405 4254 Z= 0.287 Chirality : 0.044 0.182 486 Planarity : 0.004 0.025 512 Dihedral : 3.632 12.152 420 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.75 % Allowed : 19.94 % Favored : 75.32 % 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: -0.64 (0.43), residues: 372 helix: 1.33 (0.41), residues: 168 sheet: -1.24 (0.57), residues: 78 loop : -2.30 (0.48), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 58 HIS 0.002 0.001 HIS A 154 PHE 0.014 0.002 PHE B 193 TYR 0.009 0.001 TYR B 95 ARG 0.001 0.000 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 91 MET cc_start: 0.6284 (ppp) cc_final: 0.4635 (mmt) REVERT: B 77 THR cc_start: 0.7795 (p) cc_final: 0.7521 (t) REVERT: B 166 LYS cc_start: 0.7776 (tptp) cc_final: 0.7304 (mmpt) outliers start: 15 outliers final: 11 residues processed: 61 average time/residue: 0.0930 time to fit residues: 7.6257 Evaluate side-chains 65 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 120 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.5509 > 50: distance: 7 - 16: 3.130 distance: 43 - 72: 33.867 distance: 51 - 79: 18.061 distance: 65 - 72: 32.788 distance: 72 - 73: 41.574 distance: 73 - 74: 16.734 distance: 73 - 76: 19.015 distance: 74 - 75: 7.376 distance: 74 - 79: 18.445 distance: 76 - 77: 29.831 distance: 76 - 78: 36.663 distance: 79 - 80: 15.763 distance: 80 - 81: 3.056 distance: 80 - 83: 23.899 distance: 81 - 82: 16.897 distance: 81 - 90: 12.707 distance: 83 - 84: 33.117 distance: 84 - 85: 20.833 distance: 85 - 86: 20.728 distance: 86 - 87: 9.391 distance: 87 - 88: 5.174 distance: 87 - 89: 10.072 distance: 90 - 91: 28.650 distance: 91 - 92: 33.435 distance: 91 - 94: 16.817 distance: 92 - 93: 37.375 distance: 92 - 96: 40.359 distance: 93 - 118: 31.189 distance: 94 - 95: 19.947 distance: 96 - 97: 30.761 distance: 97 - 98: 18.804 distance: 97 - 100: 3.640 distance: 98 - 99: 12.865 distance: 98 - 104: 22.368 distance: 99 - 124: 37.145 distance: 100 - 101: 37.116 distance: 101 - 102: 14.885 distance: 102 - 103: 10.206 distance: 104 - 105: 29.775 distance: 105 - 106: 42.552 distance: 105 - 108: 6.333 distance: 106 - 107: 19.890 distance: 106 - 118: 20.715 distance: 108 - 109: 4.684 distance: 109 - 110: 18.184 distance: 109 - 111: 5.750 distance: 110 - 112: 20.725 distance: 111 - 113: 10.875 distance: 112 - 113: 14.541 distance: 113 - 115: 12.858 distance: 114 - 116: 3.008 distance: 115 - 117: 10.447 distance: 116 - 117: 14.836 distance: 118 - 119: 19.290 distance: 119 - 120: 13.911 distance: 119 - 122: 15.976 distance: 120 - 121: 19.011 distance: 120 - 124: 27.116 distance: 122 - 123: 15.388 distance: 124 - 125: 30.060 distance: 125 - 126: 20.246 distance: 125 - 128: 18.741 distance: 126 - 127: 56.249 distance: 126 - 135: 15.341 distance: 128 - 129: 12.411 distance: 129 - 130: 20.785 distance: 129 - 131: 4.504 distance: 130 - 132: 8.539 distance: 131 - 133: 14.582 distance: 132 - 134: 5.629 distance: 133 - 134: 10.740 distance: 135 - 136: 37.018 distance: 136 - 137: 51.587 distance: 136 - 139: 29.139 distance: 137 - 138: 25.874 distance: 137 - 143: 61.224 distance: 139 - 140: 45.196 distance: 140 - 141: 11.999 distance: 140 - 142: 13.158 distance: 143 - 144: 18.648 distance: 143 - 149: 16.606 distance: 144 - 145: 19.906 distance: 144 - 147: 22.253 distance: 145 - 146: 17.281 distance: 145 - 150: 26.038 distance: 147 - 148: 25.402 distance: 148 - 149: 27.474 distance: 150 - 151: 17.780 distance: 151 - 152: 39.751 distance: 151 - 154: 18.317 distance: 152 - 153: 6.222 distance: 152 - 159: 27.727 distance: 154 - 155: 14.668 distance: 155 - 156: 34.069 distance: 156 - 157: 28.200 distance: 156 - 158: 7.293