Starting phenix.real_space_refine on Sun Mar 10 14:29:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c1d_30269/03_2024/7c1d_30269.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c1d_30269/03_2024/7c1d_30269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c1d_30269/03_2024/7c1d_30269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c1d_30269/03_2024/7c1d_30269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c1d_30269/03_2024/7c1d_30269.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c1d_30269/03_2024/7c1d_30269.pdb" } resolution = 3.8 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= 0.005 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: 3 Type Number sf(0) Gaussians C 1254 2.51 5 N 360 2.21 5 O 420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2034 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 339 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 339 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 339 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 339 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 339 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 339 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.43, per 1000 atoms: 0.70 Number of scatterers: 2034 At special positions: 0 Unit cell: (105.768, 61.02, 33.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 420 8.00 N 360 7.00 C 1254 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: 0.81 Conformation dependent library (CDL) restraints added in 403.9 milliseconds 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 516 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 2 sheets defined 0.0% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.602A pdb=" N ALA E 53 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA A 53 " --> pdb=" O THR B 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.585A pdb=" N ALA F 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA C 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 No hydrogen bonds 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: 0.02 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 372 1.29 - 1.36: 336 1.36 - 1.42: 54 1.42 - 1.48: 348 1.48 - 1.55: 930 Bond restraints: 2040 Sorted by residual: bond pdb=" CB VAL F 66 " pdb=" CG2 VAL F 66 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.06e-01 bond pdb=" CB VAL E 66 " pdb=" CG2 VAL E 66 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.06e-01 bond pdb=" CB VAL D 66 " pdb=" CG2 VAL D 66 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.96e-01 bond pdb=" CB VAL C 66 " pdb=" CG2 VAL C 66 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.93e-01 bond pdb=" CB VAL B 66 " pdb=" CG2 VAL B 66 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.83e-01 ... (remaining 2035 not shown) Histogram of bond angle deviations from ideal: 105.97 - 110.99: 806 110.99 - 116.02: 652 116.02 - 121.04: 601 121.04 - 126.07: 701 126.07 - 131.09: 6 Bond angle restraints: 2766 Sorted by residual: angle pdb=" N GLY F 51 " pdb=" CA GLY F 51 " pdb=" C GLY F 51 " ideal model delta sigma weight residual 110.18 115.29 -5.11 1.56e+00 4.11e-01 1.07e+01 angle pdb=" N GLY A 51 " pdb=" CA GLY A 51 " pdb=" C GLY A 51 " ideal model delta sigma weight residual 110.18 115.28 -5.10 1.56e+00 4.11e-01 1.07e+01 angle pdb=" N GLY D 51 " pdb=" CA GLY D 51 " pdb=" C GLY D 51 " ideal model delta sigma weight residual 110.18 115.24 -5.06 1.56e+00 4.11e-01 1.05e+01 angle pdb=" N GLY E 51 " pdb=" CA GLY E 51 " pdb=" C GLY E 51 " ideal model delta sigma weight residual 110.18 115.24 -5.06 1.56e+00 4.11e-01 1.05e+01 angle pdb=" N GLY B 51 " pdb=" CA GLY B 51 " pdb=" C GLY B 51 " ideal model delta sigma weight residual 110.18 115.22 -5.04 1.56e+00 4.11e-01 1.04e+01 ... (remaining 2761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 1074 16.53 - 33.05: 78 33.05 - 49.58: 18 49.58 - 66.11: 0 66.11 - 82.63: 6 Dihedral angle restraints: 1176 sinusoidal: 360 harmonic: 816 Sorted by residual: dihedral pdb=" CA ILE E 88 " pdb=" C ILE E 88 " pdb=" N ALA E 89 " pdb=" CA ALA E 89 " ideal model delta harmonic sigma weight residual 180.00 -164.12 -15.88 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ILE A 88 " pdb=" C ILE A 88 " pdb=" N ALA A 89 " pdb=" CA ALA A 89 " ideal model delta harmonic sigma weight residual 180.00 -164.14 -15.86 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ILE C 88 " pdb=" C ILE C 88 " pdb=" N ALA C 89 " pdb=" CA ALA C 89 " ideal model delta harmonic sigma weight residual -180.00 -164.15 -15.85 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 1173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 160 0.026 - 0.053: 93 0.053 - 0.079: 55 0.079 - 0.106: 28 0.106 - 0.132: 30 Chirality restraints: 366 Sorted by residual: chirality pdb=" CA VAL E 95 " pdb=" N VAL E 95 " pdb=" C VAL E 95 " pdb=" CB VAL E 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA VAL B 95 " pdb=" N VAL B 95 " pdb=" C VAL B 95 " pdb=" CB VAL B 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA VAL D 95 " pdb=" N VAL D 95 " pdb=" C VAL D 95 " pdb=" CB VAL D 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 363 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 94 " 0.008 2.00e-02 2.50e+03 6.91e-03 8.35e-01 pdb=" CG PHE D 94 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE D 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE D 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE D 94 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 94 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 94 " 0.009 2.00e-02 2.50e+03 6.85e-03 8.22e-01 pdb=" CG PHE C 94 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE C 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 94 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 94 " 0.008 2.00e-02 2.50e+03 6.81e-03 8.12e-01 pdb=" CG PHE B 94 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE B 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 94 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 94 " 0.001 2.00e-02 2.50e+03 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 852 2.87 - 3.38: 1890 3.38 - 3.89: 3196 3.89 - 4.39: 3053 4.39 - 4.90: 6398 Nonbonded interactions: 15389 Sorted by model distance: nonbonded pdb=" O GLY A 84 " pdb=" OG SER A 87 " model vdw 2.367 2.440 nonbonded pdb=" O GLY C 84 " pdb=" OG SER C 87 " model vdw 2.367 2.440 nonbonded pdb=" O GLY B 84 " pdb=" OG SER B 87 " model vdw 2.368 2.440 nonbonded pdb=" O GLY F 84 " pdb=" OG SER F 87 " model vdw 2.368 2.440 nonbonded pdb=" O GLY D 84 " pdb=" OG SER D 87 " model vdw 2.368 2.440 ... (remaining 15384 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' 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: 0.470 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: 2.250 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.160 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 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 : 0.004 0.030 2040 Z= 0.178 Angle : 0.709 5.111 2766 Z= 0.456 Chirality : 0.054 0.132 366 Planarity : 0.003 0.008 354 Dihedral : 13.995 82.631 660 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.41 % Favored : 79.59 % Rotamer: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % 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: -6.46 (0.32), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.92 (0.25), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.002 HIS F 50 PHE 0.016 0.004 PHE D 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: E 60 LYS cc_start: 0.7901 (mttt) cc_final: 0.7668 (mttp) REVERT: E 61 GLU cc_start: 0.8046 (tp30) cc_final: 0.7698 (tp30) REVERT: E 83 GLU cc_start: 0.8173 (mp0) cc_final: 0.7947 (mp0) REVERT: A 72 THR cc_start: 0.8327 (m) cc_final: 0.8093 (m) REVERT: B 83 GLU cc_start: 0.8800 (mp0) cc_final: 0.8487 (mp0) REVERT: B 92 THR cc_start: 0.8360 (m) cc_final: 0.7980 (p) REVERT: C 64 THR cc_start: 0.8989 (t) cc_final: 0.8709 (t) REVERT: C 83 GLU cc_start: 0.8624 (mp0) cc_final: 0.8400 (mp0) REVERT: D 83 GLU cc_start: 0.8555 (mp0) cc_final: 0.8146 (mp0) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1278 time to fit residues: 11.3242 Evaluate side-chains 56 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 20.0000 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- 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: 0.7092 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2040 Z= 0.109 Angle : 0.512 4.005 2766 Z= 0.293 Chirality : 0.050 0.148 366 Planarity : 0.002 0.013 354 Dihedral : 4.390 15.718 300 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.99 % Favored : 84.01 % Rotamer: Outliers : 8.85 % Allowed : 12.50 % Favored : 78.65 % 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: -5.56 (0.37), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.28), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.010 0.003 PHE D 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 52 time to evaluate : 0.224 Fit side-chains REVERT: E 60 LYS cc_start: 0.7908 (mttt) cc_final: 0.7679 (mttp) REVERT: E 61 GLU cc_start: 0.8272 (tp30) cc_final: 0.7913 (tp30) REVERT: E 83 GLU cc_start: 0.8236 (mp0) cc_final: 0.7751 (mp0) REVERT: B 79 GLN cc_start: 0.8320 (mt0) cc_final: 0.7740 (mt0) REVERT: B 83 GLU cc_start: 0.8760 (mp0) cc_final: 0.8418 (mp0) REVERT: B 92 THR cc_start: 0.8380 (m) cc_final: 0.8042 (p) REVERT: F 61 GLU cc_start: 0.7896 (tp30) cc_final: 0.7205 (tt0) REVERT: C 61 GLU cc_start: 0.8204 (tp30) cc_final: 0.6494 (tp30) REVERT: C 64 THR cc_start: 0.9174 (t) cc_final: 0.8900 (t) REVERT: C 83 GLU cc_start: 0.8533 (mp0) cc_final: 0.8318 (mp0) outliers start: 17 outliers final: 15 residues processed: 60 average time/residue: 0.0837 time to fit residues: 6.2883 Evaluate side-chains 64 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 49 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 64 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 20 optimal weight: 30.0000 chunk 14 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 2040 Z= 0.264 Angle : 0.668 4.386 2766 Z= 0.395 Chirality : 0.056 0.161 366 Planarity : 0.004 0.016 354 Dihedral : 5.701 20.217 300 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 28.57 % Favored : 71.43 % Rotamer: Outliers : 11.46 % Allowed : 13.02 % Favored : 75.52 % 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: -5.54 (0.40), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.22 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 50 PHE 0.037 0.010 PHE D 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 48 time to evaluate : 0.266 Fit side-chains REVERT: E 60 LYS cc_start: 0.8079 (mttt) cc_final: 0.7830 (mttp) REVERT: E 61 GLU cc_start: 0.7998 (tp30) cc_final: 0.7776 (tp30) REVERT: E 83 GLU cc_start: 0.8287 (mp0) cc_final: 0.8054 (mp0) REVERT: B 83 GLU cc_start: 0.8568 (mp0) cc_final: 0.8251 (mp0) REVERT: B 92 THR cc_start: 0.8655 (m) cc_final: 0.8222 (p) REVERT: F 61 GLU cc_start: 0.8019 (tp30) cc_final: 0.7277 (tt0) REVERT: C 64 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8959 (p) REVERT: C 83 GLU cc_start: 0.8324 (mp0) cc_final: 0.7930 (mp0) REVERT: D 58 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7949 (tttt) REVERT: D 83 GLU cc_start: 0.8270 (mp0) cc_final: 0.7913 (mp0) outliers start: 22 outliers final: 19 residues processed: 59 average time/residue: 0.0843 time to fit residues: 6.2906 Evaluate side-chains 65 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 45 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 64 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2040 Z= 0.250 Angle : 0.649 4.396 2766 Z= 0.383 Chirality : 0.055 0.161 366 Planarity : 0.004 0.015 354 Dihedral : 5.538 19.196 300 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.51 % Favored : 74.49 % Rotamer: Outliers : 11.98 % Allowed : 16.67 % Favored : 71.35 % 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: -5.46 (0.40), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.31), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 50 PHE 0.035 0.009 PHE D 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 50 time to evaluate : 0.226 Fit side-chains REVERT: E 60 LYS cc_start: 0.8091 (mttt) cc_final: 0.7857 (mttp) REVERT: E 61 GLU cc_start: 0.7980 (tp30) cc_final: 0.7749 (tp30) REVERT: E 83 GLU cc_start: 0.8426 (mp0) cc_final: 0.8155 (mp0) REVERT: B 58 LYS cc_start: 0.7986 (tttt) cc_final: 0.7635 (mppt) REVERT: B 83 GLU cc_start: 0.8755 (mp0) cc_final: 0.8411 (mp0) REVERT: F 61 GLU cc_start: 0.8074 (tp30) cc_final: 0.7367 (tt0) REVERT: C 64 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.9041 (p) REVERT: D 61 GLU cc_start: 0.3787 (OUTLIER) cc_final: 0.2862 (pm20) REVERT: D 83 GLU cc_start: 0.8227 (mp0) cc_final: 0.7906 (mp0) outliers start: 23 outliers final: 20 residues processed: 60 average time/residue: 0.0831 time to fit residues: 6.2792 Evaluate side-chains 69 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 47 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 64 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 20 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 2040 Z= 0.369 Angle : 0.803 4.938 2766 Z= 0.479 Chirality : 0.061 0.168 366 Planarity : 0.005 0.023 354 Dihedral : 6.498 23.548 300 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 24.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 36.05 % Favored : 63.95 % Rotamer: Outliers : 13.54 % Allowed : 20.31 % Favored : 66.15 % 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: -5.55 (0.42), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.22 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 50 PHE 0.051 0.013 PHE D 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 51 time to evaluate : 0.200 Fit side-chains REVERT: E 60 LYS cc_start: 0.8100 (mttt) cc_final: 0.7882 (mttp) REVERT: E 83 GLU cc_start: 0.8411 (mp0) cc_final: 0.7992 (mp0) REVERT: A 57 GLU cc_start: 0.7705 (tp30) cc_final: 0.7027 (pp20) REVERT: B 83 GLU cc_start: 0.8523 (mp0) cc_final: 0.8211 (mp0) REVERT: F 61 GLU cc_start: 0.7956 (tp30) cc_final: 0.7312 (tt0) REVERT: D 58 LYS cc_start: 0.7826 (mtpt) cc_final: 0.7477 (mppt) REVERT: D 61 GLU cc_start: 0.3322 (OUTLIER) cc_final: 0.2580 (pm20) REVERT: D 83 GLU cc_start: 0.7993 (mp0) cc_final: 0.7480 (mp0) outliers start: 26 outliers final: 22 residues processed: 65 average time/residue: 0.0728 time to fit residues: 5.9827 Evaluate side-chains 73 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 50 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 64 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2040 Z= 0.171 Angle : 0.586 4.130 2766 Z= 0.344 Chirality : 0.053 0.157 366 Planarity : 0.003 0.016 354 Dihedral : 5.228 18.201 300 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.77 % Favored : 78.23 % Rotamer: Outliers : 10.94 % Allowed : 23.96 % Favored : 65.10 % 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: -5.33 (0.41), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.31), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 50 PHE 0.022 0.006 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 52 time to evaluate : 0.219 Fit side-chains REVERT: E 60 LYS cc_start: 0.8089 (mttt) cc_final: 0.7876 (mttp) REVERT: E 61 GLU cc_start: 0.8019 (tp30) cc_final: 0.7811 (tp30) REVERT: E 83 GLU cc_start: 0.8430 (mp0) cc_final: 0.8167 (mp0) REVERT: A 57 GLU cc_start: 0.7502 (tp30) cc_final: 0.6710 (pp20) REVERT: B 83 GLU cc_start: 0.8777 (mp0) cc_final: 0.8429 (mp0) REVERT: F 61 GLU cc_start: 0.8069 (tp30) cc_final: 0.7364 (tt0) REVERT: C 57 GLU cc_start: 0.7759 (tp30) cc_final: 0.7479 (pp20) REVERT: D 61 GLU cc_start: 0.4212 (OUTLIER) cc_final: 0.3217 (pm20) outliers start: 21 outliers final: 19 residues processed: 61 average time/residue: 0.0745 time to fit residues: 5.7776 Evaluate side-chains 71 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 51 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 64 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 30.0000 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2040 Z= 0.122 Angle : 0.532 4.621 2766 Z= 0.310 Chirality : 0.050 0.149 366 Planarity : 0.002 0.018 354 Dihedral : 4.689 18.237 300 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.75 % Favored : 79.25 % Rotamer: Outliers : 10.42 % Allowed : 26.04 % Favored : 63.54 % 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: -5.09 (0.42), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.015 0.004 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 51 time to evaluate : 0.221 Fit side-chains REVERT: E 60 LYS cc_start: 0.8001 (mttt) cc_final: 0.7780 (mttp) REVERT: E 61 GLU cc_start: 0.8160 (tp30) cc_final: 0.7526 (tt0) REVERT: B 83 GLU cc_start: 0.8734 (mp0) cc_final: 0.8445 (mp0) REVERT: B 92 THR cc_start: 0.8443 (m) cc_final: 0.7997 (p) REVERT: F 61 GLU cc_start: 0.8195 (tp30) cc_final: 0.7581 (tt0) REVERT: C 83 GLU cc_start: 0.8194 (mp0) cc_final: 0.7712 (mp0) REVERT: D 61 GLU cc_start: 0.4104 (OUTLIER) cc_final: 0.3064 (pm20) outliers start: 20 outliers final: 17 residues processed: 61 average time/residue: 0.0856 time to fit residues: 6.5939 Evaluate side-chains 68 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 50 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 61 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 24 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2040 Z= 0.172 Angle : 0.627 7.214 2766 Z= 0.360 Chirality : 0.052 0.155 366 Planarity : 0.003 0.019 354 Dihedral : 4.896 18.132 300 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.13 % Favored : 76.87 % Rotamer: Outliers : 11.46 % Allowed : 27.08 % Favored : 61.46 % 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: -5.04 (0.42), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.023 0.006 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 49 time to evaluate : 0.185 Fit side-chains REVERT: E 60 LYS cc_start: 0.8012 (mttt) cc_final: 0.7798 (mttp) REVERT: E 61 GLU cc_start: 0.8154 (tp30) cc_final: 0.7918 (tp30) REVERT: B 83 GLU cc_start: 0.8806 (mp0) cc_final: 0.8434 (mp0) REVERT: B 92 THR cc_start: 0.8401 (m) cc_final: 0.7927 (p) REVERT: F 61 GLU cc_start: 0.8217 (tp30) cc_final: 0.7593 (tt0) REVERT: C 83 GLU cc_start: 0.8263 (mp0) cc_final: 0.7779 (mp0) REVERT: D 61 GLU cc_start: 0.4168 (OUTLIER) cc_final: 0.3116 (pm20) outliers start: 22 outliers final: 21 residues processed: 60 average time/residue: 0.0802 time to fit residues: 6.0392 Evaluate side-chains 70 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 48 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 74 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2040 Z= 0.136 Angle : 0.579 6.778 2766 Z= 0.332 Chirality : 0.050 0.152 366 Planarity : 0.003 0.019 354 Dihedral : 4.592 17.760 300 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.37 % Favored : 81.63 % Rotamer: Outliers : 10.42 % Allowed : 26.56 % Favored : 63.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.43), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.016 0.004 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 49 time to evaluate : 0.220 Fit side-chains REVERT: E 60 LYS cc_start: 0.7953 (mttt) cc_final: 0.7697 (mttp) REVERT: E 61 GLU cc_start: 0.8129 (tp30) cc_final: 0.7813 (tp30) REVERT: A 58 LYS cc_start: 0.7887 (mtpt) cc_final: 0.7607 (mtpt) REVERT: B 83 GLU cc_start: 0.8875 (mp0) cc_final: 0.8501 (mp0) REVERT: B 92 THR cc_start: 0.8253 (m) cc_final: 0.7695 (p) REVERT: F 61 GLU cc_start: 0.8246 (tp30) cc_final: 0.7604 (tt0) REVERT: C 83 GLU cc_start: 0.8267 (mp0) cc_final: 0.7800 (mp0) REVERT: D 61 GLU cc_start: 0.4091 (OUTLIER) cc_final: 0.3037 (pm20) outliers start: 20 outliers final: 19 residues processed: 58 average time/residue: 0.0798 time to fit residues: 5.9228 Evaluate side-chains 68 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 48 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 1 optimal weight: 10.0000 chunk 17 optimal weight: 0.1980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2040 Z= 0.112 Angle : 0.547 6.494 2766 Z= 0.312 Chirality : 0.049 0.147 366 Planarity : 0.002 0.020 354 Dihedral : 4.117 15.881 300 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.01 % Favored : 82.99 % Rotamer: Outliers : 9.38 % Allowed : 29.17 % Favored : 61.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.44), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.011 0.003 PHE A 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 48 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: E 60 LYS cc_start: 0.7867 (mttt) cc_final: 0.7539 (mttp) REVERT: A 58 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7812 (mtpt) REVERT: B 83 GLU cc_start: 0.8799 (mp0) cc_final: 0.8407 (mp0) REVERT: B 92 THR cc_start: 0.8301 (m) cc_final: 0.7760 (p) REVERT: F 61 GLU cc_start: 0.8308 (tp30) cc_final: 0.7686 (tt0) REVERT: C 83 GLU cc_start: 0.8282 (mp0) cc_final: 0.7849 (mp0) REVERT: D 61 GLU cc_start: 0.4028 (OUTLIER) cc_final: 0.2941 (pm20) outliers start: 18 outliers final: 16 residues processed: 57 average time/residue: 0.0776 time to fit residues: 5.6971 Evaluate side-chains 65 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 48 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 61 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 9.9990 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 0.0570 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5426 r_free = 0.5426 target = 0.352745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.5341 r_free = 0.5341 target = 0.253773 restraints weight = 2574.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.5339 r_free = 0.5339 target = 0.253108 restraints weight = 5252.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 88)----------------| | r_work = 0.5356 r_free = 0.5356 target = 0.250896 restraints weight = 5160.108| |-----------------------------------------------------------------------------| r_work (final): 0.4749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2040 Z= 0.107 Angle : 0.537 6.227 2766 Z= 0.307 Chirality : 0.049 0.146 366 Planarity : 0.002 0.020 354 Dihedral : 4.053 16.068 300 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.99 % Favored : 84.01 % Rotamer: Outliers : 9.90 % Allowed : 28.12 % Favored : 61.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.45), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.009 0.002 PHE A 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 935.43 seconds wall clock time: 17 minutes 42.81 seconds (1062.81 seconds total)