Starting phenix.real_space_refine on Wed Sep 17 02:56:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hxa_52458/09_2025/9hxa_52458.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hxa_52458/09_2025/9hxa_52458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hxa_52458/09_2025/9hxa_52458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hxa_52458/09_2025/9hxa_52458.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hxa_52458/09_2025/9hxa_52458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hxa_52458/09_2025/9hxa_52458.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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 530 2.51 5 N 148 2.21 5 O 170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 848 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 424 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Restraints were copied for chains: A Time building chain proxies: 0.18, per 1000 atoms: 0.21 Number of scatterers: 848 At special positions: 0 Unit cell: (98.44, 89.24, 20.24, 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 170 8.00 N 148 7.00 C 530 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: 0.03 Conformation dependent library (CDL) restraints added in 21.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 208 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 0.04 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: 148 1.29 - 1.35: 136 1.35 - 1.42: 34 1.42 - 1.48: 130 1.48 - 1.54: 404 Bond restraints: 852 Sorted by residual: bond pdb=" N VAL A 82 " pdb=" CA VAL A 82 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.03e+01 bond pdb=" N VAL C 82 " pdb=" CA VAL C 82 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" N VAL C 77 " pdb=" CA VAL C 77 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.28e-02 6.10e+03 7.35e+00 bond pdb=" N VAL A 77 " pdb=" CA VAL A 77 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.28e-02 6.10e+03 7.32e+00 bond pdb=" N GLN C 79 " pdb=" CA GLN C 79 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.26e-02 6.30e+03 6.61e+00 ... (remaining 847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 991 1.02 - 2.04: 125 2.04 - 3.06: 25 3.06 - 4.08: 9 4.08 - 5.10: 4 Bond angle restraints: 1154 Sorted by residual: angle pdb=" N GLU A 83 " pdb=" CA GLU A 83 " pdb=" C GLU A 83 " ideal model delta sigma weight residual 112.87 107.77 5.10 1.20e+00 6.94e-01 1.80e+01 angle pdb=" N GLU C 83 " pdb=" CA GLU C 83 " pdb=" C GLU C 83 " ideal model delta sigma weight residual 112.87 107.79 5.08 1.20e+00 6.94e-01 1.79e+01 angle pdb=" CA LYS C 80 " pdb=" C LYS C 80 " pdb=" O LYS C 80 " ideal model delta sigma weight residual 121.84 118.08 3.76 1.16e+00 7.43e-01 1.05e+01 angle pdb=" CA LYS A 80 " pdb=" C LYS A 80 " pdb=" O LYS A 80 " ideal model delta sigma weight residual 121.84 118.11 3.73 1.16e+00 7.43e-01 1.04e+01 angle pdb=" CA THR C 81 " pdb=" CB THR C 81 " pdb=" OG1 THR C 81 " ideal model delta sigma weight residual 109.60 105.10 4.50 1.50e+00 4.44e-01 8.99e+00 ... (remaining 1149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.90: 438 10.90 - 21.80: 38 21.80 - 32.70: 10 32.70 - 43.60: 4 43.60 - 54.50: 2 Dihedral angle restraints: 492 sinusoidal: 160 harmonic: 332 Sorted by residual: dihedral pdb=" CA GLU C 83 " pdb=" CB GLU C 83 " pdb=" CG GLU C 83 " pdb=" CD GLU C 83 " 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=" CA GLU A 83 " pdb=" CB GLU A 83 " pdb=" CG GLU A 83 " pdb=" CD GLU A 83 " ideal model delta sinusoidal sigma weight residual -60.00 -99.39 39.39 3 1.50e+01 4.44e-03 6.98e+00 dihedral pdb=" CA GLU C 61 " pdb=" C GLU C 61 " pdb=" N GLN C 62 " pdb=" CA GLN C 62 " ideal model delta harmonic sigma weight residual -180.00 -170.29 -9.71 0 5.00e+00 4.00e-02 3.77e+00 ... (remaining 489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 87 0.038 - 0.075: 30 0.075 - 0.113: 29 0.113 - 0.150: 0 0.150 - 0.188: 6 Chirality restraints: 152 Sorted by residual: chirality pdb=" CB VAL A 82 " pdb=" CA VAL A 82 " pdb=" CG1 VAL A 82 " pdb=" CG2 VAL A 82 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.83e-01 chirality pdb=" CA VAL C 77 " pdb=" N VAL C 77 " pdb=" C VAL C 77 " pdb=" CB VAL C 77 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.67e-01 chirality pdb=" CB VAL C 82 " pdb=" CA VAL C 82 " pdb=" CG1 VAL C 82 " pdb=" CG2 VAL C 82 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.61e-01 ... (remaining 149 not shown) Planarity restraints: 144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 38 " -0.007 2.00e-02 2.50e+03 1.30e-02 1.68e+00 pdb=" C LEU A 38 " 0.022 2.00e-02 2.50e+03 pdb=" O LEU A 38 " -0.008 2.00e-02 2.50e+03 pdb=" N TYR A 39 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 38 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.64e+00 pdb=" C LEU C 38 " 0.022 2.00e-02 2.50e+03 pdb=" O LEU C 38 " -0.008 2.00e-02 2.50e+03 pdb=" N TYR C 39 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 81 " 0.002 2.00e-02 2.50e+03 4.70e-03 2.21e-01 pdb=" C THR C 81 " -0.008 2.00e-02 2.50e+03 pdb=" O THR C 81 " 0.003 2.00e-02 2.50e+03 pdb=" N VAL C 82 " 0.003 2.00e-02 2.50e+03 ... (remaining 141 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 506 3.05 - 3.51: 692 3.51 - 3.98: 934 3.98 - 4.44: 738 4.44 - 4.90: 1420 Nonbonded interactions: 4290 Sorted by model distance: nonbonded pdb=" OG SER A 42 " pdb=" OG1 THR A 75 " model vdw 2.589 3.040 nonbonded pdb=" OG SER C 42 " pdb=" OG1 THR C 75 " model vdw 2.589 3.040 nonbonded pdb=" N GLU C 83 " pdb=" N GLY C 84 " model vdw 2.628 2.560 nonbonded pdb=" N GLU A 83 " pdb=" N GLY A 84 " model vdw 2.628 2.560 nonbonded pdb=" O SER C 42 " pdb=" OG SER C 42 " model vdw 2.655 3.040 ... (remaining 4285 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' } 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: 2.950 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: 0.010 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 1.910 Find NCS groups from input model: 0.010 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:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 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 : 0.006 0.040 852 Z= 0.420 Angle : 0.810 5.097 1154 Z= 0.533 Chirality : 0.062 0.188 152 Planarity : 0.002 0.013 144 Dihedral : 10.524 54.503 284 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 15.12 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.61 (0.70), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.53), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.002 TYR A 39 PHE 0.005 0.002 PHE A 94 HIS 0.002 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00620 ( 852) covalent geometry : angle 0.81007 ( 1154) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0275 time to fit residues: 1.1441 Evaluate side-chains 28 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 6 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 0.0470 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- 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 = 0.4813 r_free = 0.4813 target = 0.244550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.233202 restraints weight = 1050.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.236368 restraints weight = 471.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.238156 restraints weight = 262.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.239436 restraints weight = 169.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.239698 restraints weight = 116.222| |-----------------------------------------------------------------------------| r_work (final): 0.4748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 852 Z= 0.110 Angle : 0.513 5.123 1154 Z= 0.276 Chirality : 0.049 0.116 152 Planarity : 0.002 0.011 144 Dihedral : 3.857 9.430 124 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 9.30 % Allowed : 25.58 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.72), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR A 39 PHE 0.003 0.001 PHE A 94 HIS 0.001 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 852) covalent geometry : angle 0.51314 ( 1154) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.018 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 32 average time/residue: 0.0250 time to fit residues: 0.8902 Evaluate side-chains 32 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 4 optimal weight: 0.0670 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- 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 = 0.4814 r_free = 0.4814 target = 0.247471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.236590 restraints weight = 1034.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.239275 restraints weight = 438.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.241487 restraints weight = 251.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.242714 restraints weight = 151.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.243584 restraints weight = 102.730| |-----------------------------------------------------------------------------| r_work (final): 0.4761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 852 Z= 0.088 Angle : 0.506 6.329 1154 Z= 0.259 Chirality : 0.048 0.110 152 Planarity : 0.002 0.010 144 Dihedral : 3.366 8.195 124 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 11.63 % Allowed : 23.26 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.73), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR C 39 PHE 0.002 0.001 PHE A 94 HIS 0.000 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00184 ( 852) covalent geometry : angle 0.50644 ( 1154) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.022 Fit side-chains REVERT: C 43 LYS cc_start: 0.8072 (ptmt) cc_final: 0.7201 (mmtt) REVERT: A 43 LYS cc_start: 0.8070 (ptmt) cc_final: 0.7204 (mmtt) outliers start: 10 outliers final: 6 residues processed: 30 average time/residue: 0.0295 time to fit residues: 0.9738 Evaluate side-chains 31 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 0.0000 chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.4753 r_free = 0.4753 target = 0.236957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.225418 restraints weight = 1064.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.228563 restraints weight = 465.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.230336 restraints weight = 257.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.231326 restraints weight = 162.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.232065 restraints weight = 117.616| |-----------------------------------------------------------------------------| r_work (final): 0.4681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 852 Z= 0.157 Angle : 0.580 6.566 1154 Z= 0.301 Chirality : 0.049 0.142 152 Planarity : 0.002 0.010 144 Dihedral : 4.295 11.884 124 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 13.95 % Allowed : 30.23 % Favored : 55.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.71), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 39 PHE 0.004 0.001 PHE A 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 852) covalent geometry : angle 0.57997 ( 1154) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.019 Fit side-chains REVERT: C 43 LYS cc_start: 0.8125 (ptmt) cc_final: 0.7223 (mmtt) REVERT: A 43 LYS cc_start: 0.8051 (ptmt) cc_final: 0.7130 (mmtt) outliers start: 12 outliers final: 8 residues processed: 32 average time/residue: 0.0266 time to fit residues: 0.9449 Evaluate side-chains 32 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 3 optimal weight: 0.3980 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 1 optimal weight: 0.0370 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.0010 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 overall best weight: 0.6466 ------------------------------------------------------------------------------- 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 = 0.4767 r_free = 0.4767 target = 0.239704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.227648 restraints weight = 1112.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.230878 restraints weight = 473.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.232861 restraints weight = 256.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.234058 restraints weight = 157.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.234500 restraints weight = 110.137| |-----------------------------------------------------------------------------| r_work (final): 0.4701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 852 Z= 0.093 Angle : 0.564 7.939 1154 Z= 0.277 Chirality : 0.049 0.110 152 Planarity : 0.002 0.010 144 Dihedral : 3.624 10.117 124 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 10.47 % Allowed : 29.07 % Favored : 60.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.72), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.001 TYR A 39 PHE 0.001 0.000 PHE A 94 HIS 0.000 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00188 ( 852) covalent geometry : angle 0.56384 ( 1154) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.017 Fit side-chains REVERT: C 43 LYS cc_start: 0.8101 (ptmt) cc_final: 0.7216 (mmtt) REVERT: A 43 LYS cc_start: 0.8101 (ptmt) cc_final: 0.7221 (mmtt) outliers start: 9 outliers final: 7 residues processed: 29 average time/residue: 0.0254 time to fit residues: 0.8296 Evaluate side-chains 30 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 0.0870 chunk 6 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.0760 ------------------------------------------------------------------------------- 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 = 0.4756 r_free = 0.4756 target = 0.240824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.230175 restraints weight = 1049.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.233036 restraints weight = 445.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.234743 restraints weight = 236.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.235629 restraints weight = 139.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.235919 restraints weight = 98.790| |-----------------------------------------------------------------------------| r_work (final): 0.4689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 852 Z= 0.103 Angle : 0.578 8.730 1154 Z= 0.275 Chirality : 0.048 0.109 152 Planarity : 0.002 0.008 144 Dihedral : 3.606 10.620 124 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 12.79 % Allowed : 30.23 % Favored : 56.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.73), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR A 39 PHE 0.003 0.001 PHE A 94 HIS 0.001 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 852) covalent geometry : angle 0.57764 ( 1154) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.018 Fit side-chains REVERT: C 43 LYS cc_start: 0.8093 (ptmt) cc_final: 0.7200 (mmtt) REVERT: A 43 LYS cc_start: 0.8117 (ptmt) cc_final: 0.7248 (mmtt) outliers start: 11 outliers final: 8 residues processed: 31 average time/residue: 0.0263 time to fit residues: 0.9041 Evaluate side-chains 32 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 8 optimal weight: 0.0670 overall best weight: 1.0522 ------------------------------------------------------------------------------- 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 = 0.4743 r_free = 0.4743 target = 0.237565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.225666 restraints weight = 1084.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.228655 restraints weight = 463.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.230773 restraints weight = 258.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.231461 restraints weight = 159.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.232538 restraints weight = 124.688| |-----------------------------------------------------------------------------| r_work (final): 0.4677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 852 Z= 0.100 Angle : 0.565 8.360 1154 Z= 0.275 Chirality : 0.047 0.109 152 Planarity : 0.002 0.013 144 Dihedral : 3.597 10.792 124 Min Nonbonded Distance : 2.661 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 11.63 % Allowed : 32.56 % Favored : 55.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.74), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.001 TYR C 39 PHE 0.002 0.001 PHE C 94 HIS 0.001 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 852) covalent geometry : angle 0.56486 ( 1154) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.032 Fit side-chains REVERT: C 43 LYS cc_start: 0.8112 (ptmt) cc_final: 0.7238 (mmtt) REVERT: A 43 LYS cc_start: 0.8101 (ptmt) cc_final: 0.7224 (mmtt) outliers start: 10 outliers final: 9 residues processed: 31 average time/residue: 0.0258 time to fit residues: 0.8943 Evaluate side-chains 33 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.4693 r_free = 0.4693 target = 0.230632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.217945 restraints weight = 1104.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.221269 restraints weight = 489.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.223074 restraints weight = 267.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.223983 restraints weight = 173.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.224299 restraints weight = 131.700| |-----------------------------------------------------------------------------| r_work (final): 0.4603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 852 Z= 0.265 Angle : 0.740 7.903 1154 Z= 0.382 Chirality : 0.052 0.182 152 Planarity : 0.003 0.013 144 Dihedral : 5.149 15.711 124 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 11.63 % Allowed : 36.05 % Favored : 52.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.43 (0.74), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.003 TYR A 39 PHE 0.004 0.001 PHE A 94 HIS 0.004 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00589 ( 852) covalent geometry : angle 0.74023 ( 1154) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 THR cc_start: 0.9113 (p) cc_final: 0.8835 (p) outliers start: 10 outliers final: 8 residues processed: 38 average time/residue: 0.0523 time to fit residues: 2.1734 Evaluate side-chains 37 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 8 optimal weight: 0.2980 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.4727 r_free = 0.4727 target = 0.235648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.223932 restraints weight = 1082.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.226912 restraints weight = 461.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.228424 restraints weight = 250.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.229614 restraints weight = 165.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.230137 restraints weight = 116.492| |-----------------------------------------------------------------------------| r_work (final): 0.4657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 852 Z= 0.134 Angle : 0.637 8.478 1154 Z= 0.321 Chirality : 0.050 0.121 152 Planarity : 0.002 0.013 144 Dihedral : 4.429 13.433 124 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 11.63 % Allowed : 36.05 % Favored : 52.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.30 (0.75), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 39 PHE 0.003 0.001 PHE C 94 HIS 0.001 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 852) covalent geometry : angle 0.63674 ( 1154) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.8163 (ptmt) cc_final: 0.7293 (mmtt) REVERT: A 43 LYS cc_start: 0.8191 (ptmt) cc_final: 0.7368 (mmtt) outliers start: 10 outliers final: 8 residues processed: 34 average time/residue: 0.0518 time to fit residues: 1.9190 Evaluate side-chains 36 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 6 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.0980 chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 0.0370 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.0060 ------------------------------------------------------------------------------- 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 = 0.4734 r_free = 0.4734 target = 0.235107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.222838 restraints weight = 1065.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.226056 restraints weight = 458.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.227846 restraints weight = 245.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.228779 restraints weight = 154.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.229303 restraints weight = 114.385| |-----------------------------------------------------------------------------| r_work (final): 0.4653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 852 Z= 0.110 Angle : 0.642 9.607 1154 Z= 0.310 Chirality : 0.049 0.110 152 Planarity : 0.002 0.012 144 Dihedral : 4.026 13.244 124 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 11.63 % Allowed : 32.56 % Favored : 55.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.29 (0.76), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR A 39 PHE 0.002 0.001 PHE C 94 HIS 0.001 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 852) covalent geometry : angle 0.64184 ( 1154) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.8136 (ptmt) cc_final: 0.7243 (mmtt) REVERT: A 43 LYS cc_start: 0.8163 (ptmt) cc_final: 0.7324 (mmtt) outliers start: 10 outliers final: 10 residues processed: 36 average time/residue: 0.0508 time to fit residues: 1.9982 Evaluate side-chains 40 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 4 optimal weight: 0.0470 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 0.3980 overall best weight: 1.6682 ------------------------------------------------------------------------------- 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 = 0.4729 r_free = 0.4729 target = 0.235475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.223770 restraints weight = 1073.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.226835 restraints weight = 459.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.228551 restraints weight = 246.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.229610 restraints weight = 154.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.229963 restraints weight = 110.822| |-----------------------------------------------------------------------------| r_work (final): 0.4649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 852 Z= 0.134 Angle : 0.645 9.205 1154 Z= 0.316 Chirality : 0.049 0.114 152 Planarity : 0.002 0.012 144 Dihedral : 4.197 13.532 124 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 11.63 % Allowed : 33.72 % Favored : 54.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.74), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 39 PHE 0.003 0.001 PHE C 94 HIS 0.001 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 852) covalent geometry : angle 0.64479 ( 1154) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 408.41 seconds wall clock time: 7 minutes 59.06 seconds (479.06 seconds total)