Starting phenix.real_space_refine on Mon Feb 10 19:26:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tif_41286/02_2025/8tif_41286.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tif_41286/02_2025/8tif_41286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tif_41286/02_2025/8tif_41286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tif_41286/02_2025/8tif_41286.map" model { file = "/net/cci-nas-00/data/ceres_data/8tif_41286/02_2025/8tif_41286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tif_41286/02_2025/8tif_41286.cif" } resolution = 3.89 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 559 2.51 5 N 146 2.21 5 O 184 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: 889 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 889 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Time building chain proxies: 0.83, per 1000 atoms: 0.93 Number of scatterers: 889 At special positions: 0 Unit cell: (47.52, 47.52, 99.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 184 8.00 N 146 7.00 C 559 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: 0.21 Conformation dependent library (CDL) restraints added in 129.1 milliseconds 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 226 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 3 sheets defined 29.8% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 13 through 46 removed outlier: 3.552A pdb=" N VAL A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 119 removed outlier: 3.617A pdb=" N VAL A 119 " --> pdb=" O GLN A 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 59 removed outlier: 7.004A pdb=" N THR A 126 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA A 81 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN A 128 " --> pdb=" O THR A 79 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 81 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 45 hydrogen bonds defined for protein. 126 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: 0.21 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 146 1.29 - 1.35: 144 1.35 - 1.42: 45 1.42 - 1.48: 154 1.48 - 1.54: 404 Bond restraints: 893 Sorted by residual: bond pdb=" CB ILE A 29 " pdb=" CG2 ILE A 29 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.20e-01 bond pdb=" CB GLN A 116 " pdb=" CG GLN A 116 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.16e-01 bond pdb=" CG1 ILE A 96 " pdb=" CD1 ILE A 96 " ideal model delta sigma weight residual 1.513 1.482 0.031 3.90e-02 6.57e+02 6.16e-01 bond pdb=" CB THR A 45 " pdb=" CG2 THR A 45 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.10e-01 bond pdb=" CG LEU A 129 " pdb=" CD1 LEU A 129 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 5.05e-01 ... (remaining 888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 1159 0.97 - 1.94: 46 1.94 - 2.91: 11 2.91 - 3.88: 4 3.88 - 4.84: 3 Bond angle restraints: 1223 Sorted by residual: angle pdb=" CB GLN A 128 " pdb=" CG GLN A 128 " pdb=" CD GLN A 128 " ideal model delta sigma weight residual 112.60 116.85 -4.25 1.70e+00 3.46e-01 6.26e+00 angle pdb=" CA GLN A 116 " pdb=" CB GLN A 116 " pdb=" CG GLN A 116 " ideal model delta sigma weight residual 114.10 118.94 -4.84 2.00e+00 2.50e-01 5.87e+00 angle pdb=" CA GLN A 128 " pdb=" CB GLN A 128 " pdb=" CG GLN A 128 " ideal model delta sigma weight residual 114.10 117.88 -3.78 2.00e+00 2.50e-01 3.56e+00 angle pdb=" CD1 LEU A 20 " pdb=" CG LEU A 20 " pdb=" CD2 LEU A 20 " ideal model delta sigma weight residual 110.80 106.76 4.04 2.20e+00 2.07e-01 3.38e+00 angle pdb=" C ALA A 19 " pdb=" N LEU A 20 " pdb=" CA LEU A 20 " ideal model delta sigma weight residual 120.29 118.21 2.08 1.42e+00 4.96e-01 2.15e+00 ... (remaining 1218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.75: 428 15.75 - 31.51: 63 31.51 - 47.26: 15 47.26 - 63.02: 4 63.02 - 78.77: 2 Dihedral angle restraints: 512 sinusoidal: 155 harmonic: 357 Sorted by residual: dihedral pdb=" CA LYS A 70 " pdb=" CB LYS A 70 " pdb=" CG LYS A 70 " pdb=" CD LYS A 70 " ideal model delta sinusoidal sigma weight residual -60.00 -111.52 51.52 3 1.50e+01 4.44e-03 9.02e+00 dihedral pdb=" N LEU A 31 " pdb=" CA LEU A 31 " pdb=" CB LEU A 31 " pdb=" CG LEU A 31 " ideal model delta sinusoidal sigma weight residual -60.00 -107.85 47.85 3 1.50e+01 4.44e-03 8.55e+00 dihedral pdb=" N ASN A 117 " pdb=" CA ASN A 117 " pdb=" CB ASN A 117 " pdb=" CG ASN A 117 " ideal model delta sinusoidal sigma weight residual 180.00 -133.83 -46.17 3 1.50e+01 4.44e-03 8.29e+00 ... (remaining 509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 111 0.033 - 0.067: 41 0.067 - 0.100: 17 0.100 - 0.134: 5 0.134 - 0.167: 1 Chirality restraints: 175 Sorted by residual: chirality pdb=" CA ILE A 96 " pdb=" N ILE A 96 " pdb=" C ILE A 96 " pdb=" CB ILE A 96 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CA ILE A 140 " pdb=" N ILE A 140 " pdb=" C ILE A 140 " pdb=" CB ILE A 140 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE A 83 " pdb=" N ILE A 83 " pdb=" C ILE A 83 " pdb=" CB ILE A 83 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 172 not shown) Planarity restraints: 150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 103 " 0.011 2.00e-02 2.50e+03 1.04e-02 2.16e+00 pdb=" CG TYR A 103 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 103 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 103 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 103 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 103 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 103 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 103 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 41 " -0.012 2.00e-02 2.50e+03 9.80e-03 1.68e+00 pdb=" CG PHE A 41 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 41 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 41 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 41 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 41 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 41 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 90 " -0.005 2.00e-02 2.50e+03 1.07e-02 1.15e+00 pdb=" C VAL A 90 " 0.019 2.00e-02 2.50e+03 pdb=" O VAL A 90 " -0.007 2.00e-02 2.50e+03 pdb=" N SER A 91 " -0.006 2.00e-02 2.50e+03 ... (remaining 147 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 338 2.83 - 3.35: 817 3.35 - 3.87: 1399 3.87 - 4.38: 1319 4.38 - 4.90: 2520 Nonbonded interactions: 6393 Sorted by model distance: nonbonded pdb=" O LEU A 118 " pdb=" OG SER A 121 " model vdw 2.317 3.040 nonbonded pdb=" NE2 GLN A 52 " pdb=" O GLY A 54 " model vdw 2.333 3.120 nonbonded pdb=" OG1 THR A 76 " pdb=" OG SER A 130 " model vdw 2.413 3.040 nonbonded pdb=" O THR A 72 " pdb=" OG1 THR A 72 " model vdw 2.443 3.040 nonbonded pdb=" OG1 THR A 76 " pdb=" N GLN A 77 " model vdw 2.512 3.120 ... (remaining 6388 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.090 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 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 : 0.005 0.031 893 Z= 0.320 Angle : 0.547 4.844 1223 Z= 0.301 Chirality : 0.044 0.167 175 Planarity : 0.002 0.011 150 Dihedral : 17.043 78.773 286 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.02 % Allowed : 43.88 % Favored : 55.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.74), residues: 129 helix: 3.77 (0.73), residues: 34 sheet: -1.42 (0.89), residues: 37 loop : -1.10 (0.73), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.002 PHE A 41 TYR 0.025 0.007 TYR A 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.096 Fit side-chains REVERT: A 128 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7834 (tp40) outliers start: 1 outliers final: 1 residues processed: 5 average time/residue: 0.1015 time to fit residues: 0.7118 Evaluate side-chains 5 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 10 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.2939 r_free = 0.2939 target = 0.069266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.062589 restraints weight = 3019.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.063938 restraints weight = 1546.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.064854 restraints weight = 956.852| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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 0.024 893 Z= 0.214 Angle : 0.469 4.705 1223 Z= 0.247 Chirality : 0.041 0.135 175 Planarity : 0.002 0.007 150 Dihedral : 5.026 40.306 134 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.02 % Allowed : 39.80 % Favored : 59.18 % 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: 0.54 (0.78), residues: 129 helix: 4.42 (0.68), residues: 34 sheet: -1.20 (0.85), residues: 44 loop : -1.02 (0.81), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE A 41 TYR 0.014 0.004 TYR A 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 8 time to evaluate : 0.106 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 9 average time/residue: 0.0779 time to fit residues: 0.9204 Evaluate side-chains 7 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 6 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.068013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.061227 restraints weight = 2963.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.062613 restraints weight = 1512.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.063545 restraints weight = 933.302| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 893 Z= 0.278 Angle : 0.464 3.593 1223 Z= 0.245 Chirality : 0.042 0.137 175 Planarity : 0.002 0.006 150 Dihedral : 3.402 10.724 132 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 5.10 % Allowed : 33.67 % Favored : 61.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.76), residues: 129 helix: 4.31 (0.67), residues: 34 sheet: -1.18 (0.83), residues: 44 loop : -1.25 (0.80), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE A 41 TYR 0.007 0.003 TYR A 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 7 time to evaluate : 0.093 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 12 average time/residue: 0.0669 time to fit residues: 1.0329 Evaluate side-chains 8 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 6 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 134 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 0.2980 chunk 4 optimal weight: 8.9990 chunk 10 optimal weight: 0.0170 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 0 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- 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 = 0.2984 r_free = 0.2984 target = 0.072554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.066060 restraints weight = 2915.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.067390 restraints weight = 1528.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.068267 restraints weight = 940.562| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 893 Z= 0.122 Angle : 0.370 3.771 1223 Z= 0.203 Chirality : 0.040 0.132 175 Planarity : 0.001 0.004 150 Dihedral : 2.918 8.953 132 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.02 % Allowed : 36.73 % Favored : 62.24 % 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: 0.49 (0.77), residues: 129 helix: 4.44 (0.72), residues: 34 sheet: -1.02 (0.82), residues: 44 loop : -1.32 (0.81), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE A 41 TYR 0.006 0.002 TYR A 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 7 time to evaluate : 0.074 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 8 average time/residue: 0.0620 time to fit residues: 0.6577 Evaluate side-chains 7 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.2944 r_free = 0.2944 target = 0.070472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.063837 restraints weight = 2926.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.065232 restraints weight = 1474.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.066145 restraints weight = 897.100| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 893 Z= 0.202 Angle : 0.426 5.424 1223 Z= 0.219 Chirality : 0.041 0.125 175 Planarity : 0.001 0.005 150 Dihedral : 2.976 9.797 132 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.08 % Allowed : 36.73 % Favored : 59.18 % 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 (0.77), residues: 129 helix: 4.34 (0.72), residues: 34 sheet: -1.08 (0.81), residues: 44 loop : -1.29 (0.81), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE A 41 TYR 0.011 0.003 TYR A 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 6 time to evaluate : 0.091 Fit side-chains REVERT: A 44 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8157 (t80) outliers start: 4 outliers final: 2 residues processed: 10 average time/residue: 0.0831 time to fit residues: 1.0570 Evaluate side-chains 9 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 6 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 4 optimal weight: 0.0770 chunk 10 optimal weight: 0.0670 chunk 5 optimal weight: 5.9990 overall best weight: 0.8078 ------------------------------------------------------------------------------- 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 = 0.2983 r_free = 0.2983 target = 0.072258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.065746 restraints weight = 2890.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.067096 restraints weight = 1530.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.067984 restraints weight = 948.083| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 893 Z= 0.121 Angle : 0.383 4.832 1223 Z= 0.199 Chirality : 0.040 0.122 175 Planarity : 0.001 0.003 150 Dihedral : 2.739 8.920 132 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 5.10 % Allowed : 36.73 % Favored : 58.16 % 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: 0.56 (0.77), residues: 129 helix: 4.42 (0.74), residues: 34 sheet: -0.91 (0.80), residues: 44 loop : -1.29 (0.81), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE A 44 TYR 0.008 0.002 TYR A 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 7 time to evaluate : 0.091 Fit side-chains REVERT: A 44 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8122 (t80) outliers start: 5 outliers final: 3 residues processed: 11 average time/residue: 0.0726 time to fit residues: 1.0254 Evaluate side-chains 11 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 7 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.0670 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- 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 = 0.2978 r_free = 0.2978 target = 0.071943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.064893 restraints weight = 2978.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.066335 restraints weight = 1539.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.067319 restraints weight = 960.374| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 893 Z= 0.144 Angle : 0.410 4.558 1223 Z= 0.216 Chirality : 0.041 0.123 175 Planarity : 0.001 0.010 150 Dihedral : 2.703 9.142 132 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.08 % Allowed : 37.76 % Favored : 58.16 % 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: 0.67 (0.77), residues: 129 helix: 4.43 (0.74), residues: 34 sheet: -0.78 (0.80), residues: 44 loop : -1.22 (0.82), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.000 PHE A 41 TYR 0.009 0.003 TYR A 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 7 time to evaluate : 0.084 Fit side-chains REVERT: A 44 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8084 (t80) outliers start: 4 outliers final: 3 residues processed: 10 average time/residue: 0.0735 time to fit residues: 0.9396 Evaluate side-chains 11 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 7 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 8 optimal weight: 0.1980 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- 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 = 0.2928 r_free = 0.2928 target = 0.069757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.063219 restraints weight = 2901.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.064623 restraints weight = 1462.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.065513 restraints weight = 881.458| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 893 Z= 0.225 Angle : 0.444 4.703 1223 Z= 0.235 Chirality : 0.041 0.127 175 Planarity : 0.001 0.009 150 Dihedral : 2.927 9.795 132 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 5.10 % Allowed : 36.73 % Favored : 58.16 % 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: 0.62 (0.77), residues: 129 helix: 4.31 (0.74), residues: 34 sheet: -0.86 (0.79), residues: 44 loop : -1.13 (0.84), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE A 41 TYR 0.011 0.003 TYR A 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 6 time to evaluate : 0.093 Fit side-chains REVERT: A 44 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8188 (t80) outliers start: 5 outliers final: 4 residues processed: 11 average time/residue: 0.0732 time to fit residues: 1.0464 Evaluate side-chains 11 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 6 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 134 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 4 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.2947 r_free = 0.2947 target = 0.070581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.063870 restraints weight = 2952.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.065292 restraints weight = 1478.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.066227 restraints weight = 889.288| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 893 Z= 0.167 Angle : 0.417 5.127 1223 Z= 0.220 Chirality : 0.041 0.124 175 Planarity : 0.001 0.008 150 Dihedral : 2.801 9.340 132 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 5.10 % Allowed : 36.73 % Favored : 58.16 % 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: 0.72 (0.77), residues: 129 helix: 4.32 (0.75), residues: 34 sheet: -0.77 (0.80), residues: 44 loop : -1.04 (0.83), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE A 41 TYR 0.010 0.003 TYR A 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 6 time to evaluate : 0.102 Fit side-chains REVERT: A 44 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8220 (t80) outliers start: 5 outliers final: 4 residues processed: 11 average time/residue: 0.0766 time to fit residues: 1.0785 Evaluate side-chains 11 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 6 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 134 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 0.0870 chunk 5 optimal weight: 4.9990 overall best weight: 2.9764 ------------------------------------------------------------------------------- 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 = 0.2882 r_free = 0.2882 target = 0.067513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.060832 restraints weight = 3088.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.062226 restraints weight = 1525.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.063137 restraints weight = 920.931| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 893 Z= 0.309 Angle : 0.487 5.082 1223 Z= 0.259 Chirality : 0.042 0.130 175 Planarity : 0.002 0.009 150 Dihedral : 3.207 10.323 132 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 5.10 % Allowed : 36.73 % Favored : 58.16 % 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: 0.63 (0.75), residues: 129 helix: 4.11 (0.73), residues: 34 sheet: -0.84 (0.79), residues: 44 loop : -0.98 (0.83), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE A 41 TYR 0.013 0.004 TYR A 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 6 time to evaluate : 0.100 Fit side-chains REVERT: A 44 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8168 (t80) outliers start: 5 outliers final: 4 residues processed: 11 average time/residue: 0.0773 time to fit residues: 1.0838 Evaluate side-chains 11 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 6 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 134 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.2887 r_free = 0.2887 target = 0.067747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.061140 restraints weight = 3062.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.062523 restraints weight = 1534.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.063365 restraints weight = 929.559| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 893 Z= 0.266 Angle : 0.466 5.201 1223 Z= 0.247 Chirality : 0.041 0.128 175 Planarity : 0.001 0.008 150 Dihedral : 3.176 10.333 132 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 5.10 % Allowed : 36.73 % Favored : 58.16 % 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: 0.67 (0.76), residues: 129 helix: 4.09 (0.73), residues: 34 sheet: -0.80 (0.79), residues: 44 loop : -0.93 (0.84), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE A 41 TYR 0.013 0.004 TYR A 103 =============================================================================== Job complete usr+sys time: 810.67 seconds wall clock time: 15 minutes 48.78 seconds (948.78 seconds total)