Starting phenix.real_space_refine on Mon Feb 10 19:26:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a05_15048/02_2025/8a05_15048.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a05_15048/02_2025/8a05_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/cci-nas-00/data/ceres_data/8a05_15048/02_2025/8a05_15048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a05_15048/02_2025/8a05_15048.map" model { file = "/net/cci-nas-00/data/ceres_data/8a05_15048/02_2025/8a05_15048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a05_15048/02_2025/8a05_15048.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 0.88, per 1000 atoms: 1.15 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.12 Conformation dependent library (CDL) restraints added in 307.1 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: 0.07 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: 0.11 Time building geometry restraints manager: 0.16 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: 0.00 - 0.87: 1007 0.87 - 1.73: 48 1.73 - 2.60: 4 2.60 - 3.46: 3 3.46 - 4.33: 1 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 3.040 nonbonded pdb=" ND2 ASN P 71 " pdb=" O UNK X 2 " model vdw 2.435 3.120 nonbonded pdb=" OD1 ASN P 19 " pdb=" OH TYR P 25 " model vdw 2.525 3.040 nonbonded pdb=" O SER P 55 " pdb=" OG SER P 55 " model vdw 2.593 3.040 nonbonded pdb=" OG SER P 37 " pdb=" NH2 ARG P 44 " model vdw 2.616 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 6.380 Find NCS groups from input model: 0.000 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:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 9.140 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.063 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0846 time to fit residues: 1.9028 Evaluate side-chains 18 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.063 ------------------------------------------------------------------------------- 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: 9.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.128394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.114169 restraints weight = 1046.383| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.96 r_work: 0.3160 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.0804 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 : 0.430 4.212 1063 Z= 0.240 Chirality : 0.045 0.121 119 Planarity : 0.004 0.025 138 Dihedral : 2.801 9.385 101 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.69 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: 0.44 (0.80), residues: 89 helix: 3.63 (1.31), residues: 9 sheet: 0.84 (1.48), residues: 14 loop : -0.31 (0.67), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE P 34 TYR 0.003 0.001 TYR P 53 ARG 0.000 0.000 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 18 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.081 Fit side-chains REVERT: P 77 TYR cc_start: 0.8786 (m-10) cc_final: 0.8534 (m-10) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.0901 time to fit residues: 1.8868 Evaluate side-chains 18 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.086 ------------------------------------------------------------------------------- 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: 8.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.0770 chunk 6 optimal weight: 8.9990 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.127458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.113263 restraints weight = 1084.170| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.02 r_work: 0.3153 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 782 Z= 0.168 Angle : 0.420 4.375 1063 Z= 0.232 Chirality : 0.045 0.123 119 Planarity : 0.004 0.023 138 Dihedral : 2.670 9.381 101 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.20 % Allowed : 13.25 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.79), residues: 89 helix: 3.82 (1.32), residues: 9 sheet: 1.09 (1.43), residues: 14 loop : -0.33 (0.66), 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 11 ARG 0.000 0.000 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 19 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.085 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.0771 time to fit residues: 1.7424 Evaluate side-chains 18 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 60 SER 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: 4.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.0470 chunk 8 optimal weight: 2.9990 overall best weight: 0.6605 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.127443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.113329 restraints weight = 1058.545| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.00 r_work: 0.3150 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1197 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= 0.171 Angle : 0.419 4.422 1063 Z= 0.231 Chirality : 0.045 0.122 119 Planarity : 0.003 0.021 138 Dihedral : 2.629 9.337 101 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.20 % Allowed : 18.07 % Favored : 80.72 % 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: 0.56 (0.79), residues: 89 helix: 3.79 (1.37), residues: 9 sheet: 1.21 (1.40), residues: 14 loop : -0.32 (0.66), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE P 34 TYR 0.002 0.000 TYR P 11 ARG 0.000 0.000 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 18 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.081 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.0882 time to fit residues: 1.8402 Evaluate side-chains 18 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.080 ------------------------------------------------------------------------------- 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: 0.7980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.4488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.123649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.109273 restraints weight = 1049.822| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.99 r_work: 0.3095 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1258 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= 0.206 Angle : 0.453 4.389 1063 Z= 0.251 Chirality : 0.046 0.125 119 Planarity : 0.003 0.020 138 Dihedral : 2.813 9.649 101 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.20 % Allowed : 18.07 % Favored : 80.72 % 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: 3.43 (1.39), residues: 9 sheet: 1.09 (1.42), residues: 14 loop : -0.38 (0.65), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE P 39 TYR 0.005 0.001 TYR P 53 ARG 0.000 0.000 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 16 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.085 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.0626 time to fit residues: 1.2441 Evaluate side-chains 16 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 60 SER 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: 10.0000 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.7488 ------------------------------------------------------------------------------- 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 = 0.3339 r_free = 0.3339 target = 0.123808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.109662 restraints weight = 1044.406| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.93 r_work: 0.3104 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 782 Z= 0.226 Angle : 0.466 4.330 1063 Z= 0.259 Chirality : 0.046 0.123 119 Planarity : 0.003 0.021 138 Dihedral : 2.914 9.847 101 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.20 % Allowed : 21.69 % Favored : 77.11 % 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: 0.29 (0.77), residues: 89 helix: 3.36 (1.38), residues: 9 sheet: 0.94 (1.41), residues: 14 loop : -0.45 (0.64), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE P 39 TYR 0.005 0.001 TYR P 77 ARG 0.000 0.000 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 16 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.090 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.0676 time to fit residues: 1.3365 Evaluate side-chains 16 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 60 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 1.1483 ------------------------------------------------------------------------------- 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 = 0.3353 r_free = 0.3353 target = 0.124927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.110866 restraints weight = 1038.946| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.92 r_work: 0.3129 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1175 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= 0.190 Angle : 0.445 4.319 1063 Z= 0.247 Chirality : 0.046 0.123 119 Planarity : 0.003 0.023 138 Dihedral : 2.825 9.457 101 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.20 % Allowed : 20.48 % 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: 0.33 (0.77), residues: 89 helix: 3.37 (1.39), residues: 9 sheet: 1.03 (1.42), residues: 14 loop : -0.43 (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 0.000 0.000 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 16 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.086 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.0659 time to fit residues: 1.3024 Evaluate side-chains 16 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.090 ------------------------------------------------------------------------------- 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: 5.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.2235 ------------------------------------------------------------------------------- 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 = 0.3349 r_free = 0.3349 target = 0.124427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.109775 restraints weight = 1070.444| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.05 r_work: 0.3112 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1183 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= 0.194 Angle : 0.454 4.318 1063 Z= 0.251 Chirality : 0.046 0.123 119 Planarity : 0.003 0.023 138 Dihedral : 2.826 9.468 101 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.20 % Allowed : 21.69 % Favored : 77.11 % 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: 0.26 (0.77), residues: 89 helix: 3.17 (1.41), residues: 9 sheet: 0.98 (1.41), residues: 14 loop : -0.46 (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 0.000 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 16 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.086 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.0627 time to fit residues: 1.2321 Evaluate side-chains 16 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 60 SER 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: 4.9990 chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.4238 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.123995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.109666 restraints weight = 1064.869| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.99 r_work: 0.3121 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1216 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= 0.206 Angle : 0.462 4.331 1063 Z= 0.256 Chirality : 0.046 0.123 119 Planarity : 0.003 0.023 138 Dihedral : 2.862 9.533 101 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.20 % Allowed : 21.69 % Favored : 77.11 % 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: 0.24 (0.77), residues: 89 helix: 3.13 (1.41), residues: 9 sheet: 1.00 (1.42), residues: 14 loop : -0.48 (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 0.000 0.000 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 16 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.090 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.0693 time to fit residues: 1.3640 Evaluate side-chains 16 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.0970 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 overall best weight: 0.7483 ------------------------------------------------------------------------------- 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 = 0.3365 r_free = 0.3365 target = 0.125921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.111519 restraints weight = 1082.116| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.01 r_work: 0.3148 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1305 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 : 0.442 4.327 1063 Z= 0.245 Chirality : 0.046 0.122 119 Planarity : 0.003 0.024 138 Dihedral : 2.753 9.536 101 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.20 % Allowed : 21.69 % Favored : 77.11 % 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 (0.77), residues: 89 helix: 3.30 (1.41), residues: 9 sheet: 1.03 (1.39), residues: 14 loop : -0.44 (0.64), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE P 34 TYR 0.004 0.001 TYR P 77 ARG 0.000 0.000 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 17 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.072 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.0640 time to fit residues: 1.3372 Evaluate side-chains 17 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 60 SER 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: 4.9990 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.128049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.113899 restraints weight = 1070.485| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.00 r_work: 0.3167 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1219 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= 0.172 Angle : 0.437 4.298 1063 Z= 0.241 Chirality : 0.046 0.123 119 Planarity : 0.003 0.024 138 Dihedral : 2.660 9.492 101 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.20 % Allowed : 22.89 % Favored : 75.90 % 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: 0.37 (0.77), residues: 89 helix: 3.43 (1.46), residues: 9 sheet: 1.12 (1.39), residues: 14 loop : -0.42 (0.64), 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 0.000 0.000 ARG P 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 817.73 seconds wall clock time: 15 minutes 38.74 seconds (938.74 seconds total)