Starting phenix.real_space_refine on Sun Mar 10 14:16:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a05_15048/03_2024/8a05_15048.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a05_15048/03_2024/8a05_15048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a05_15048/03_2024/8a05_15048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a05_15048/03_2024/8a05_15048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a05_15048/03_2024/8a05_15048.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a05_15048/03_2024/8a05_15048.pdb" } resolution = 3.4 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 2 5.16 5 C 502 2.51 5 N 116 2.21 5 O 144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 764 Number of models: 1 Model: "" Number of chains: 2 Chain: "P" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 739 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "X" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 0.84, per 1000 atoms: 1.10 Number of scatterers: 764 At special positions: 0 Unit cell: (45.88, 45.88, 54.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 2 16.00 O 144 8.00 N 116 7.00 C 502 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: 0.28 Conformation dependent library (CDL) restraints added in 163.1 milliseconds 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 182 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 2 sheets defined 16.5% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'P' and resid 55 through 64 removed outlier: 3.572A pdb=" N LEU P 59 " --> pdb=" O SER P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 74 through 78 removed outlier: 3.666A pdb=" N TYR P 77 " --> pdb=" O PRO P 74 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 13 through 17 removed outlier: 6.445A pdb=" N ILE P 7 " --> pdb=" O ILE P 35 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE P 35 " --> pdb=" O ILE P 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 24 through 26 removed outlier: 4.649A pdb=" N PHE P 24 " --> pdb=" O PHE P 87 " (cutoff:3.500A) 19 hydrogen bonds defined for protein. 45 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: 0.14 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 239 1.34 - 1.46: 190 1.46 - 1.57: 349 1.57 - 1.69: 0 1.69 - 1.80: 4 Bond restraints: 782 Sorted by residual: bond pdb=" C LEU P 56 " pdb=" N PRO P 57 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.36e-02 5.41e+03 4.18e-01 bond pdb=" CB PRO P 74 " pdb=" CG PRO P 74 " ideal model delta sigma weight residual 1.492 1.523 -0.031 5.00e-02 4.00e+02 3.81e-01 bond pdb=" N GLU P 22 " pdb=" CA GLU P 22 " ideal model delta sigma weight residual 1.460 1.469 -0.009 1.54e-02 4.22e+03 3.75e-01 bond pdb=" CA UNK X 1 " pdb=" CB UNK X 1 " ideal model delta sigma weight residual 1.530 1.520 0.010 2.00e-02 2.50e+03 2.67e-01 bond pdb=" CA LEU P 56 " pdb=" C LEU P 56 " ideal model delta sigma weight residual 1.522 1.528 -0.007 1.26e-02 6.30e+03 2.67e-01 ... (remaining 777 not shown) Histogram of bond angle deviations from ideal: 100.91 - 106.59: 17 106.59 - 112.27: 359 112.27 - 117.96: 184 117.96 - 123.64: 495 123.64 - 129.33: 8 Bond angle restraints: 1063 Sorted by residual: angle pdb=" C SER P 21 " pdb=" N GLU P 22 " pdb=" CA GLU P 22 " ideal model delta sigma weight residual 122.46 124.74 -2.28 1.41e+00 5.03e-01 2.61e+00 angle pdb=" CA GLU P 22 " pdb=" CB GLU P 22 " pdb=" CG GLU P 22 " ideal model delta sigma weight residual 114.10 116.83 -2.73 2.00e+00 2.50e-01 1.87e+00 angle pdb=" C GLN P 30 " pdb=" CA GLN P 30 " pdb=" CB GLN P 30 " ideal model delta sigma weight residual 110.06 108.50 1.56 1.44e+00 4.82e-01 1.18e+00 angle pdb=" C ILE P 29 " pdb=" N GLN P 30 " pdb=" CA GLN P 30 " ideal model delta sigma weight residual 126.45 128.34 -1.89 1.77e+00 3.19e-01 1.14e+00 angle pdb=" C LEU P 56 " pdb=" N PRO P 57 " pdb=" CD PRO P 57 " ideal model delta sigma weight residual 125.00 129.33 -4.33 4.10e+00 5.95e-02 1.11e+00 ... (remaining 1058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.71: 378 11.71 - 23.42: 55 23.42 - 35.14: 15 35.14 - 46.85: 2 46.85 - 58.56: 3 Dihedral angle restraints: 453 sinusoidal: 171 harmonic: 282 Sorted by residual: dihedral pdb=" CA ASN P 19 " pdb=" CB ASN P 19 " pdb=" CG ASN P 19 " pdb=" OD1 ASN P 19 " ideal model delta sinusoidal sigma weight residual 120.00 178.56 -58.56 2 2.00e+01 2.50e-03 8.73e+00 dihedral pdb=" N GLN P 5 " pdb=" CA GLN P 5 " pdb=" CB GLN P 5 " pdb=" CG GLN P 5 " ideal model delta sinusoidal sigma weight residual -60.00 -99.40 39.40 3 1.50e+01 4.44e-03 6.98e+00 dihedral pdb=" N ASN P 88 " pdb=" CA ASN P 88 " pdb=" CB ASN P 88 " pdb=" CG ASN P 88 " ideal model delta sinusoidal sigma weight residual -60.00 -98.11 38.11 3 1.50e+01 4.44e-03 6.69e+00 ... (remaining 450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 58 0.025 - 0.050: 29 0.050 - 0.076: 17 0.076 - 0.101: 9 0.101 - 0.126: 6 Chirality restraints: 119 Sorted by residual: chirality pdb=" CA VAL P 38 " pdb=" N VAL P 38 " pdb=" C VAL P 38 " pdb=" CB VAL P 38 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE P 40 " pdb=" N ILE P 40 " pdb=" C ILE P 40 " pdb=" CB ILE P 40 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA VAL P 15 " pdb=" N VAL P 15 " pdb=" C VAL P 15 " pdb=" CB VAL P 15 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 116 not shown) Planarity restraints: 138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE P 73 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.64e+00 pdb=" N PRO P 74 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO P 74 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO P 74 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU P 56 " -0.015 5.00e-02 4.00e+02 2.24e-02 8.01e-01 pdb=" N PRO P 57 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO P 57 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO P 57 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR P 31 " 0.013 5.00e-02 4.00e+02 1.96e-02 6.13e-01 pdb=" N PRO P 32 " -0.034 5.00e-02 4.00e+02 pdb=" CA PRO P 32 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO P 32 " 0.011 5.00e-02 4.00e+02 ... (remaining 135 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 261 2.84 - 3.36: 647 3.36 - 3.87: 1110 3.87 - 4.39: 1263 4.39 - 4.90: 2268 Nonbonded interactions: 5549 Sorted by model distance: nonbonded pdb=" O THR P 80 " pdb=" OG1 THR P 83 " model vdw 2.328 2.440 nonbonded pdb=" ND2 ASN P 71 " pdb=" O UNK X 2 " model vdw 2.435 2.520 nonbonded pdb=" OD1 ASN P 19 " pdb=" OH TYR P 25 " model vdw 2.525 2.440 nonbonded pdb=" O SER P 55 " pdb=" OG SER P 55 " model vdw 2.593 2.440 nonbonded pdb=" OG SER P 37 " pdb=" NH2 ARG P 44 " model vdw 2.616 2.520 ... (remaining 5544 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.730 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.310 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 0.031 782 Z= 0.176 Angle : 0.429 4.327 1063 Z= 0.238 Chirality : 0.047 0.126 119 Planarity : 0.004 0.032 138 Dihedral : 12.668 58.559 271 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.83), residues: 89 helix: 3.75 (1.54), residues: 9 sheet: 0.56 (1.47), residues: 14 loop : -0.28 (0.69), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE P 39 TYR 0.003 0.001 TYR P 53 ARG 0.001 0.001 ARG P 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 83 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.087 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1080 time to fit residues: 2.4362 Evaluate side-chains 18 residues out of total 83 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 0.0770 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.5183 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 782 Z= 0.210 Angle : 0.446 4.221 1063 Z= 0.249 Chirality : 0.046 0.124 119 Planarity : 0.004 0.025 138 Dihedral : 2.913 9.430 101 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.20 % Allowed : 9.64 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.80), residues: 89 helix: 3.49 (1.34), residues: 9 sheet: 0.75 (1.50), residues: 14 loop : -0.32 (0.66), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE P 39 TYR 0.004 0.001 TYR P 53 ARG 0.002 0.001 ARG P 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 83 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.091 Fit side-chains REVERT: P 77 TYR cc_start: 0.8625 (m-10) cc_final: 0.8393 (m-10) outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.0727 time to fit residues: 1.4240 Evaluate side-chains 16 residues out of total 83 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 60 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.4488 ------------------------------------------------------------------------------- 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: 0.8241 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 782 Z= 0.207 Angle : 0.441 4.347 1063 Z= 0.245 Chirality : 0.046 0.124 119 Planarity : 0.004 0.024 138 Dihedral : 2.863 9.400 101 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.41 % Allowed : 14.46 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.78), residues: 89 helix: 3.64 (1.32), residues: 9 sheet: 0.79 (1.45), residues: 14 loop : -0.41 (0.64), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE P 39 TYR 0.003 0.001 TYR P 53 ARG 0.001 0.001 ARG P 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 83 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.096 Fit side-chains REVERT: P 77 TYR cc_start: 0.8660 (m-10) cc_final: 0.8325 (m-10) outliers start: 2 outliers final: 2 residues processed: 18 average time/residue: 0.0891 time to fit residues: 1.8668 Evaluate side-chains 18 residues out of total 83 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 76 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.8735 ------------------------------------------------------------------------------- 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: 0.8206 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 782 Z= 0.178 Angle : 0.422 4.380 1063 Z= 0.233 Chirality : 0.046 0.123 119 Planarity : 0.004 0.022 138 Dihedral : 2.750 9.501 101 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.20 % Allowed : 15.66 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.78), residues: 89 helix: 3.86 (1.31), residues: 9 sheet: 0.89 (1.44), residues: 14 loop : -0.42 (0.65), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE P 34 TYR 0.002 0.000 TYR P 53 ARG 0.001 0.001 ARG P 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 83 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.089 Fit side-chains REVERT: P 77 TYR cc_start: 0.8646 (m-10) cc_final: 0.8259 (m-10) outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.0960 time to fit residues: 1.7861 Evaluate side-chains 16 residues out of total 83 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 60 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.0770 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.0670 overall best weight: 1.5355 ------------------------------------------------------------------------------- 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: 0.8234 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 782 Z= 0.210 Angle : 0.450 4.409 1063 Z= 0.247 Chirality : 0.046 0.123 119 Planarity : 0.003 0.021 138 Dihedral : 2.832 9.482 101 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.41 % Allowed : 19.28 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.79), residues: 89 helix: 4.04 (1.37), residues: 9 sheet: 0.94 (1.45), residues: 14 loop : -0.42 (0.65), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE P 39 TYR 0.004 0.001 TYR P 53 ARG 0.001 0.001 ARG P 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 83 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.088 Fit side-chains REVERT: P 77 TYR cc_start: 0.8636 (m-10) cc_final: 0.8227 (m-10) outliers start: 2 outliers final: 2 residues processed: 18 average time/residue: 0.0897 time to fit residues: 1.8852 Evaluate side-chains 18 residues out of total 83 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 76 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 overall best weight: 1.3985 ------------------------------------------------------------------------------- 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: 0.8232 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 782 Z= 0.203 Angle : 0.446 4.390 1063 Z= 0.245 Chirality : 0.046 0.124 119 Planarity : 0.003 0.022 138 Dihedral : 2.816 9.405 101 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.61 % Allowed : 21.69 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.78), residues: 89 helix: 3.48 (1.37), residues: 9 sheet: 0.93 (1.46), residues: 14 loop : -0.44 (0.64), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE P 39 TYR 0.004 0.001 TYR P 53 ARG 0.001 0.001 ARG P 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 83 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.081 Fit side-chains REVERT: P 77 TYR cc_start: 0.8631 (m-10) cc_final: 0.8226 (m-10) outliers start: 3 outliers final: 3 residues processed: 18 average time/residue: 0.0863 time to fit residues: 1.8101 Evaluate side-chains 19 residues out of total 83 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 76 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.1488 ------------------------------------------------------------------------------- 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: 0.8223 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 782 Z= 0.188 Angle : 0.435 4.368 1063 Z= 0.238 Chirality : 0.046 0.124 119 Planarity : 0.003 0.022 138 Dihedral : 2.793 9.337 101 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.20 % Allowed : 27.71 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.78), residues: 89 helix: 3.58 (1.40), residues: 9 sheet: 0.92 (1.44), residues: 14 loop : -0.44 (0.64), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE P 39 TYR 0.003 0.001 TYR P 53 ARG 0.001 0.001 ARG P 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 83 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.089 Fit side-chains REVERT: P 77 TYR cc_start: 0.8631 (m-10) cc_final: 0.8208 (m-10) outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.0908 time to fit residues: 1.7958 Evaluate side-chains 17 residues out of total 83 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 60 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 overall best weight: 0.7230 ------------------------------------------------------------------------------- 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: 0.8191 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 782 Z= 0.169 Angle : 0.418 4.365 1063 Z= 0.228 Chirality : 0.046 0.122 119 Planarity : 0.003 0.022 138 Dihedral : 2.702 9.463 101 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.41 % Allowed : 26.51 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.78), residues: 89 helix: 3.78 (1.41), residues: 9 sheet: 1.00 (1.41), residues: 14 loop : -0.42 (0.65), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE P 39 TYR 0.002 0.000 TYR P 53 ARG 0.001 0.000 ARG P 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 83 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.091 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 18 average time/residue: 0.0929 time to fit residues: 1.9482 Evaluate side-chains 18 residues out of total 83 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 76 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.1235 ------------------------------------------------------------------------------- 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: 0.8211 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 782 Z= 0.186 Angle : 0.433 4.351 1063 Z= 0.238 Chirality : 0.046 0.123 119 Planarity : 0.003 0.022 138 Dihedral : 2.752 9.770 101 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.41 % Allowed : 26.51 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.78), residues: 89 helix: 3.71 (1.42), residues: 9 sheet: 0.97 (1.42), residues: 14 loop : -0.41 (0.65), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE P 39 TYR 0.003 0.001 TYR P 53 ARG 0.001 0.001 ARG P 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 83 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.093 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 0.0657 time to fit residues: 1.3724 Evaluate side-chains 17 residues out of total 83 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 76 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.2485 ------------------------------------------------------------------------------- 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: 0.8219 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 782 Z= 0.193 Angle : 0.445 4.403 1063 Z= 0.244 Chirality : 0.046 0.124 119 Planarity : 0.003 0.021 138 Dihedral : 2.804 9.785 101 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.41 % Allowed : 26.51 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.79), residues: 89 helix: 3.99 (1.43), residues: 9 sheet: 0.91 (1.42), residues: 14 loop : -0.42 (0.65), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE P 34 TYR 0.005 0.001 TYR P 77 ARG 0.001 0.001 ARG P 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 178 Ramachandran restraints generated. 89 Oldfield, 0 Emsley, 89 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 83 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.089 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 18 average time/residue: 0.0885 time to fit residues: 1.8527 Evaluate side-chains 18 residues out of total 83 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 76 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.0870 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 overall best weight: 0.8455 ------------------------------------------------------------------------------- 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 = 0.3363 r_free = 0.3363 target = 0.125863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.111306 restraints weight = 1048.277| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.98 r_work: 0.3131 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 782 Z= 0.176 Angle : 0.441 4.368 1063 Z= 0.241 Chirality : 0.046 0.123 119 Planarity : 0.003 0.023 138 Dihedral : 2.743 9.682 101 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.41 % Allowed : 26.51 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.78), residues: 89 helix: 3.48 (1.41), residues: 9 sheet: 0.94 (1.42), residues: 14 loop : -0.41 (0.65), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE P 50 TYR 0.003 0.001 TYR P 53 ARG 0.001 0.001 ARG P 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 672.80 seconds wall clock time: 13 minutes 26.96 seconds (806.96 seconds total)