Starting phenix.real_space_refine on Thu Dec 7 15:48:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4a_31705/12_2023/7v4a_31705.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4a_31705/12_2023/7v4a_31705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4a_31705/12_2023/7v4a_31705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4a_31705/12_2023/7v4a_31705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4a_31705/12_2023/7v4a_31705.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4a_31705/12_2023/7v4a_31705.pdb" } resolution = 3.2 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= 0.003 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 1029 2.51 5 N 294 2.21 5 O 330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "B GLU 20": "OE1" <-> "OE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 1653 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 551 Classifications: {'peptide': 80} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 79} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 551 Classifications: {'peptide': 80} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 79} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 551 Classifications: {'peptide': 80} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 79} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 1.35, per 1000 atoms: 0.82 Number of scatterers: 1653 At special positions: 0 Unit cell: (67.84, 86.92, 34.98, 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 330 8.00 N 294 7.00 C 1029 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: 0.63 Conformation dependent library (CDL) restraints added in 328.8 milliseconds 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 402 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 removed outlier: 6.702A pdb=" N ALA A 18 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA B 18 " --> pdb=" O ALA C 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 23 removed outlier: 6.620A pdb=" N THR A 22 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR B 22 " --> pdb=" O LYS C 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 37 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 6.604A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLY B 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N HIS A 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA B 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N VAL A 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N VAL B 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N THR A 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLY C 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N HIS B 50 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA C 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N VAL B 52 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N VAL C 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N THR B 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 63 through 66 removed outlier: 6.744A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N VAL B 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN A 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N VAL C 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 72 removed outlier: 6.729A pdb=" N ALA A 69 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N THR B 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A 71 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA B 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N THR C 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL B 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 75 through 79 Processing sheet with id=AA8, first strand: chain 'A' and resid 86 through 91 30 hydrogen bonds defined for protein. 90 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: 0.32 Time building geometry restraints manager: 0.69 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: 291 1.29 - 1.36: 258 1.36 - 1.42: 51 1.42 - 1.48: 270 1.48 - 1.55: 786 Bond restraints: 1656 Sorted by residual: bond pdb=" CA GLU C 83 " pdb=" CB GLU C 83 " ideal model delta sigma weight residual 1.533 1.549 -0.016 1.63e-02 3.76e+03 9.11e-01 bond pdb=" CA GLU B 83 " pdb=" CB GLU B 83 " ideal model delta sigma weight residual 1.533 1.548 -0.015 1.63e-02 3.76e+03 8.64e-01 bond pdb=" CA GLU A 83 " pdb=" CB GLU A 83 " ideal model delta sigma weight residual 1.533 1.547 -0.014 1.63e-02 3.76e+03 7.79e-01 bond pdb=" CB ASP C 98 " pdb=" CG ASP C 98 " ideal model delta sigma weight residual 1.516 1.502 0.014 2.50e-02 1.60e+03 3.35e-01 bond pdb=" CA GLN C 62 " pdb=" C GLN C 62 " ideal model delta sigma weight residual 1.530 1.524 0.006 1.08e-02 8.57e+03 3.27e-01 ... (remaining 1651 not shown) Histogram of bond angle deviations from ideal: 106.09 - 111.12: 677 111.12 - 116.15: 534 116.15 - 121.18: 463 121.18 - 126.21: 546 126.21 - 131.24: 3 Bond angle restraints: 2223 Sorted by residual: angle pdb=" CA GLU A 83 " pdb=" CB GLU A 83 " pdb=" CG GLU A 83 " ideal model delta sigma weight residual 114.10 118.57 -4.47 2.00e+00 2.50e-01 5.00e+00 angle pdb=" CA GLU B 83 " pdb=" CB GLU B 83 " pdb=" CG GLU B 83 " ideal model delta sigma weight residual 114.10 118.57 -4.47 2.00e+00 2.50e-01 4.99e+00 angle pdb=" CA GLU C 83 " pdb=" CB GLU C 83 " pdb=" CG GLU C 83 " ideal model delta sigma weight residual 114.10 118.55 -4.45 2.00e+00 2.50e-01 4.94e+00 angle pdb=" C GLU C 83 " pdb=" CA GLU C 83 " pdb=" CB GLU C 83 " ideal model delta sigma weight residual 110.44 107.32 3.12 1.68e+00 3.54e-01 3.46e+00 angle pdb=" C GLU A 83 " pdb=" CA GLU A 83 " pdb=" CB GLU A 83 " ideal model delta sigma weight residual 110.44 107.33 3.11 1.68e+00 3.54e-01 3.44e+00 ... (remaining 2218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 912 17.48 - 34.95: 45 34.95 - 52.42: 15 52.42 - 69.89: 3 69.89 - 87.37: 3 Dihedral angle restraints: 978 sinusoidal: 339 harmonic: 639 Sorted by residual: dihedral pdb=" CB GLU B 20 " pdb=" CG GLU B 20 " pdb=" CD GLU B 20 " pdb=" OE1 GLU B 20 " ideal model delta sinusoidal sigma weight residual 0.00 87.37 -87.37 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU C 20 " pdb=" CG GLU C 20 " pdb=" CD GLU C 20 " pdb=" OE1 GLU C 20 " ideal model delta sinusoidal sigma weight residual 0.00 87.36 -87.36 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU A 20 " pdb=" CG GLU A 20 " pdb=" CD GLU A 20 " pdb=" OE1 GLU A 20 " ideal model delta sinusoidal sigma weight residual 0.00 87.32 -87.32 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 134 0.026 - 0.052: 81 0.052 - 0.077: 22 0.077 - 0.103: 25 0.103 - 0.128: 23 Chirality restraints: 285 Sorted by residual: chirality pdb=" CA VAL C 15 " pdb=" N VAL C 15 " pdb=" C VAL C 15 " pdb=" CB VAL C 15 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA VAL A 15 " pdb=" N VAL A 15 " pdb=" C VAL A 15 " pdb=" CB VAL A 15 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE B 88 " pdb=" N ILE B 88 " pdb=" C ILE B 88 " pdb=" CB ILE B 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 282 not shown) Planarity restraints: 276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 83 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.08e+00 pdb=" CD GLU C 83 " -0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU C 83 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU C 83 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 83 " 0.008 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" CD GLU A 83 " -0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU A 83 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 83 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 83 " 0.008 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" CD GLU B 83 " -0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU B 83 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU B 83 " 0.011 2.00e-02 2.50e+03 ... (remaining 273 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 667 2.92 - 3.41: 1441 3.41 - 3.91: 2358 3.91 - 4.40: 2385 4.40 - 4.90: 5063 Nonbonded interactions: 11914 Sorted by model distance: nonbonded pdb=" N ASP A 98 " pdb=" OD1 ASP A 98 " model vdw 2.423 2.520 nonbonded pdb=" N ASP C 98 " pdb=" OD1 ASP C 98 " model vdw 2.423 2.520 nonbonded pdb=" N ASP B 98 " pdb=" OD1 ASP B 98 " model vdw 2.424 2.520 nonbonded pdb=" N GLU A 83 " pdb=" OE1 GLU A 83 " model vdw 2.444 2.520 nonbonded pdb=" N GLU B 83 " pdb=" OE1 GLU B 83 " model vdw 2.445 2.520 ... (remaining 11909 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 4.690 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.780 Find NCS groups from input model: 0.110 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1656 Z= 0.152 Angle : 0.518 4.471 2223 Z= 0.314 Chirality : 0.052 0.128 285 Planarity : 0.002 0.018 276 Dihedral : 14.278 87.365 576 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % 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: -5.80 (0.26), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.41 (0.20), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.001 0.000 PHE C 94 TYR 0.005 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.191 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1864 time to fit residues: 14.4911 Evaluate side-chains 50 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.154 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.0270 chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 0.0470 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 1656 Z= 0.147 Angle : 0.493 4.360 2223 Z= 0.284 Chirality : 0.050 0.122 285 Planarity : 0.003 0.015 276 Dihedral : 4.165 13.384 237 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.64 % Allowed : 21.21 % Favored : 75.15 % 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: -5.20 (0.31), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.24), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 50 PHE 0.001 0.000 PHE B 94 TYR 0.012 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.189 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 56 average time/residue: 0.1345 time to fit residues: 8.5632 Evaluate side-chains 53 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.195 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0196 time to fit residues: 0.4182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.0070 chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- 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: 0.7893 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 1656 Z= 0.148 Angle : 0.462 5.136 2223 Z= 0.265 Chirality : 0.049 0.121 285 Planarity : 0.002 0.014 276 Dihedral : 4.045 13.280 237 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.24 % Allowed : 22.42 % Favored : 73.33 % 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: -4.90 (0.34), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.26), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.002 0.000 PHE B 94 TYR 0.009 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.202 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 51 average time/residue: 0.1248 time to fit residues: 7.3306 Evaluate side-chains 49 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.192 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0192 time to fit residues: 0.3601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.7892 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1656 Z= 0.158 Angle : 0.439 5.678 2223 Z= 0.251 Chirality : 0.048 0.122 285 Planarity : 0.002 0.009 276 Dihedral : 4.029 13.414 237 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 8.48 % Allowed : 22.42 % Favored : 69.09 % 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: -4.67 (0.35), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.27), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.003 0.001 PHE B 94 TYR 0.009 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 0.196 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 57 average time/residue: 0.1200 time to fit residues: 7.9607 Evaluate side-chains 59 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.205 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0239 time to fit residues: 0.6346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 7 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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: 0.7930 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1656 Z= 0.252 Angle : 0.525 5.830 2223 Z= 0.299 Chirality : 0.049 0.124 285 Planarity : 0.002 0.014 276 Dihedral : 4.654 14.876 237 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 3.03 % Allowed : 26.06 % Favored : 70.91 % 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: -4.68 (0.34), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.26), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.004 0.001 PHE B 94 TYR 0.012 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.177 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 49 average time/residue: 0.1289 time to fit residues: 7.2578 Evaluate side-chains 48 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.185 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0221 time to fit residues: 0.3513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 19 optimal weight: 0.0040 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 overall best weight: 2.0998 ------------------------------------------------------------------------------- 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: 0.7931 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1656 Z= 0.288 Angle : 0.528 4.763 2223 Z= 0.305 Chirality : 0.049 0.126 285 Planarity : 0.002 0.010 276 Dihedral : 4.906 15.647 237 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 3.64 % Allowed : 26.06 % Favored : 70.30 % 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: -4.59 (0.35), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.27), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.004 0.001 PHE B 94 TYR 0.013 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.186 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 49 average time/residue: 0.1293 time to fit residues: 7.2687 Evaluate side-chains 49 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.186 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1091 time to fit residues: 0.6109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 1656 Z= 0.425 Angle : 0.646 5.404 2223 Z= 0.370 Chirality : 0.052 0.131 285 Planarity : 0.003 0.017 276 Dihedral : 5.451 18.377 237 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.60 % Favored : 86.40 % Rotamer: Outliers : 5.45 % Allowed : 26.67 % Favored : 67.88 % 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 (0.35), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.26), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.004 0.001 PHE B 94 TYR 0.013 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.188 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 51 average time/residue: 0.1170 time to fit residues: 6.9097 Evaluate side-chains 52 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.181 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0221 time to fit residues: 0.4855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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: 0.7892 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1656 Z= 0.176 Angle : 0.520 4.546 2223 Z= 0.296 Chirality : 0.049 0.129 285 Planarity : 0.002 0.017 276 Dihedral : 4.692 16.241 237 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 0.61 % Allowed : 27.88 % Favored : 71.52 % 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: -4.49 (0.36), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.28), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.002 0.000 PHE B 94 TYR 0.011 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.116 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 45 average time/residue: 0.0831 time to fit residues: 4.3110 Evaluate side-chains 45 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.116 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0131 time to fit residues: 0.2466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 0.2980 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7835 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 1656 Z= 0.157 Angle : 0.483 7.311 2223 Z= 0.277 Chirality : 0.049 0.126 285 Planarity : 0.002 0.027 276 Dihedral : 4.054 16.735 237 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 0.00 % Allowed : 32.12 % Favored : 67.88 % 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: -4.18 (0.39), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.30), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.002 0.000 PHE B 94 TYR 0.009 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.193 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1147 time to fit residues: 6.1988 Evaluate side-chains 45 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.194 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.0470 chunk 16 optimal weight: 0.0370 chunk 1 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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: 0.7854 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 1656 Z= 0.191 Angle : 0.553 7.563 2223 Z= 0.308 Chirality : 0.048 0.125 285 Planarity : 0.002 0.026 276 Dihedral : 4.121 16.118 237 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 0.00 % Allowed : 34.55 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.41), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.31), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.002 0.001 PHE B 94 TYR 0.009 0.002 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.190 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1167 time to fit residues: 5.8565 Evaluate side-chains 43 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.186 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.145920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.118254 restraints weight = 2253.088| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 3.36 r_work: 0.3730 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 1656 Z= 0.216 Angle : 0.528 6.720 2223 Z= 0.300 Chirality : 0.049 0.125 285 Planarity : 0.002 0.024 276 Dihedral : 4.374 16.471 237 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 0.61 % Allowed : 31.52 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.41), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.31), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.003 0.001 PHE B 94 TYR 0.010 0.002 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 949.29 seconds wall clock time: 21 minutes 52.18 seconds (1312.18 seconds total)