Starting phenix.real_space_refine on Wed Sep 17 02:59:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hgr_52165/09_2025/9hgr_52165.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hgr_52165/09_2025/9hgr_52165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hgr_52165/09_2025/9hgr_52165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hgr_52165/09_2025/9hgr_52165.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hgr_52165/09_2025/9hgr_52165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hgr_52165/09_2025/9hgr_52165.map" } resolution = 2.7 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= 0.004 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 598 2.51 5 N 168 2.21 5 O 194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s 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: 960 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 480 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain breaks: 1 Restraints were copied for chains: B Time building chain proxies: 0.59, per 1000 atoms: 0.61 Number of scatterers: 960 At special positions: 0 Unit cell: (109.48, 92.92, 22.08, 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 194 8.00 N 168 7.00 C 598 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: 0.15 Conformation dependent library (CDL) restraints added in 217.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 236 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: 0.29 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: 0.15 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: 170 1.29 - 1.35: 151 1.35 - 1.42: 33 1.42 - 1.48: 158 1.48 - 1.54: 450 Bond restraints: 962 Sorted by residual: bond pdb=" N ALA A 56 " pdb=" CA ALA A 56 " ideal model delta sigma weight residual 1.455 1.482 -0.027 1.27e-02 6.20e+03 4.46e+00 bond pdb=" N ALA B 56 " pdb=" CA ALA B 56 " ideal model delta sigma weight residual 1.455 1.482 -0.027 1.27e-02 6.20e+03 4.45e+00 bond pdb=" N GLU B 57 " pdb=" CA GLU B 57 " ideal model delta sigma weight residual 1.458 1.484 -0.027 1.28e-02 6.10e+03 4.38e+00 bond pdb=" N GLU A 57 " pdb=" CA GLU A 57 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.28e-02 6.10e+03 4.25e+00 bond pdb=" CA ALA A 56 " pdb=" CB ALA A 56 " ideal model delta sigma weight residual 1.534 1.509 0.025 1.76e-02 3.23e+03 1.99e+00 ... (remaining 957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 1250 0.96 - 1.93: 36 1.93 - 2.89: 8 2.89 - 3.86: 2 3.86 - 4.82: 2 Bond angle restraints: 1298 Sorted by residual: angle pdb=" N GLU B 57 " pdb=" CA GLU B 57 " pdb=" C GLU B 57 " ideal model delta sigma weight residual 113.12 108.30 4.82 1.25e+00 6.40e-01 1.49e+01 angle pdb=" N GLU A 57 " pdb=" CA GLU A 57 " pdb=" C GLU A 57 " ideal model delta sigma weight residual 113.12 108.35 4.77 1.25e+00 6.40e-01 1.46e+01 angle pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" O ALA A 56 " ideal model delta sigma weight residual 121.33 118.99 2.34 1.08e+00 8.57e-01 4.71e+00 angle pdb=" CA ALA B 56 " pdb=" C ALA B 56 " pdb=" O ALA B 56 " ideal model delta sigma weight residual 121.33 119.00 2.33 1.08e+00 8.57e-01 4.66e+00 angle pdb=" C GLY A 93 " pdb=" N PHE A 94 " pdb=" CA PHE A 94 " ideal model delta sigma weight residual 121.70 124.82 -3.12 1.80e+00 3.09e-01 3.00e+00 ... (remaining 1293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.46: 502 13.46 - 26.93: 32 26.93 - 40.39: 10 40.39 - 53.85: 4 53.85 - 67.32: 8 Dihedral angle restraints: 556 sinusoidal: 180 harmonic: 376 Sorted by residual: dihedral pdb=" CA GLU B 61 " pdb=" CB GLU B 61 " pdb=" CG GLU B 61 " pdb=" CD GLU B 61 " ideal model delta sinusoidal sigma weight residual 60.00 115.57 -55.57 3 1.50e+01 4.44e-03 9.35e+00 dihedral pdb=" CA GLU A 61 " pdb=" CB GLU A 61 " pdb=" CG GLU A 61 " pdb=" CD GLU A 61 " ideal model delta sinusoidal sigma weight residual 60.00 115.56 -55.56 3 1.50e+01 4.44e-03 9.35e+00 dihedral pdb=" CA LYS B 80 " pdb=" CB LYS B 80 " pdb=" CG LYS B 80 " pdb=" CD LYS B 80 " ideal model delta sinusoidal sigma weight residual 180.00 130.22 49.78 3 1.50e+01 4.44e-03 8.82e+00 ... (remaining 553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 76 0.024 - 0.048: 48 0.048 - 0.072: 12 0.072 - 0.096: 14 0.096 - 0.120: 20 Chirality restraints: 170 Sorted by residual: chirality pdb=" CA GLU B 57 " pdb=" N GLU B 57 " pdb=" C GLU B 57 " pdb=" CB GLU B 57 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA ILE B 88 " pdb=" N ILE B 88 " pdb=" C ILE B 88 " pdb=" CB ILE B 88 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.40e-01 ... (remaining 167 not shown) Planarity restraints: 162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 70 " 0.004 2.00e-02 2.50e+03 7.66e-03 5.86e-01 pdb=" C VAL A 70 " -0.013 2.00e-02 2.50e+03 pdb=" O VAL A 70 " 0.005 2.00e-02 2.50e+03 pdb=" N VAL A 71 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 70 " 0.004 2.00e-02 2.50e+03 7.61e-03 5.79e-01 pdb=" C VAL B 70 " -0.013 2.00e-02 2.50e+03 pdb=" O VAL B 70 " 0.005 2.00e-02 2.50e+03 pdb=" N VAL B 71 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 39 " -0.004 2.00e-02 2.50e+03 3.45e-03 2.38e-01 pdb=" CG TYR B 39 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR B 39 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 39 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 39 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 39 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 39 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 39 " -0.000 2.00e-02 2.50e+03 ... (remaining 159 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.03: 518 3.03 - 3.50: 748 3.50 - 3.97: 1074 3.97 - 4.43: 897 4.43 - 4.90: 1573 Nonbonded interactions: 4810 Sorted by model distance: nonbonded pdb=" O THR A 22 " pdb=" OG1 THR A 22 " model vdw 2.569 3.040 nonbonded pdb=" O THR B 22 " pdb=" OG1 THR B 22 " model vdw 2.569 3.040 nonbonded pdb=" C THR A 44 " pdb=" OG1 THR A 44 " model vdw 2.657 2.616 nonbonded pdb=" C THR B 44 " pdb=" OG1 THR B 44 " model vdw 2.658 2.616 nonbonded pdb=" C THR B 92 " pdb=" OG1 THR B 92 " model vdw 2.658 2.616 ... (remaining 4805 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 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.950 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: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.090 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:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 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 : 0.003 0.027 962 Z= 0.198 Angle : 0.471 4.823 1298 Z= 0.305 Chirality : 0.051 0.120 170 Planarity : 0.001 0.008 162 Dihedral : 14.287 67.318 320 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 23.40 % Favored : 76.60 % 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: -3.44 (0.60), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.46), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR B 39 PHE 0.008 0.002 PHE B 94 HIS 0.001 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 962) covalent geometry : angle 0.47102 ( 1298) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.037 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.3866 time to fit residues: 7.8628 Evaluate side-chains 18 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 13 optimal weight: 0.0570 chunk 6 optimal weight: 0.0050 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.0870 chunk 9 optimal weight: 0.0060 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.1706 ------------------------------------------------------------------------------- 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 = 0.4639 r_free = 0.4639 target = 0.219712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.207095 restraints weight = 870.464| |-----------------------------------------------------------------------------| r_work (start): 0.4480 rms_B_bonded: 1.79 r_work: 0.4412 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.4330 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 962 Z= 0.057 Angle : 0.330 2.976 1298 Z= 0.188 Chirality : 0.049 0.115 170 Planarity : 0.001 0.006 162 Dihedral : 2.510 5.968 140 Min Nonbonded Distance : 2.661 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 6.38 % Allowed : 19.15 % Favored : 74.47 % 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: -3.40 (0.61), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.47), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR B 39 PHE 0.007 0.002 PHE B 94 HIS 0.000 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00106 ( 962) covalent geometry : angle 0.33043 ( 1298) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.037 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 22 average time/residue: 0.3089 time to fit residues: 6.9391 Evaluate side-chains 23 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 63 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 0.0060 chunk 1 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 = 0.4619 r_free = 0.4619 target = 0.217249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.204189 restraints weight = 870.586| |-----------------------------------------------------------------------------| r_work (start): 0.4457 rms_B_bonded: 1.84 r_work: 0.4381 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4296 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 962 Z= 0.063 Angle : 0.329 3.011 1298 Z= 0.187 Chirality : 0.048 0.115 170 Planarity : 0.001 0.006 162 Dihedral : 2.757 5.938 140 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 12.77 % Allowed : 10.64 % Favored : 76.60 % 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: -3.31 (0.62), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.48), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR B 39 PHE 0.008 0.002 PHE A 94 HIS 0.000 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00119 ( 962) covalent geometry : angle 0.32854 ( 1298) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 17 time to evaluate : 0.038 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 27 average time/residue: 0.2702 time to fit residues: 7.4598 Evaluate side-chains 24 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 63 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.0030 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- 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 = 0.4556 r_free = 0.4556 target = 0.210636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.196949 restraints weight = 854.089| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 1.79 r_work: 0.4303 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4212 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 962 Z= 0.165 Angle : 0.456 3.154 1298 Z= 0.256 Chirality : 0.050 0.114 170 Planarity : 0.002 0.013 162 Dihedral : 4.276 10.211 140 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.94 % Favored : 88.06 % Rotamer: Outliers : 7.45 % Allowed : 15.96 % Favored : 76.60 % 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: -3.54 (0.60), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.45), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR B 39 PHE 0.011 0.004 PHE A 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 962) covalent geometry : angle 0.45635 ( 1298) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.036 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 24 average time/residue: 0.3772 time to fit residues: 9.2030 Evaluate side-chains 27 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.4544 r_free = 0.4544 target = 0.209185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.195453 restraints weight = 856.379| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 1.89 r_work: 0.4294 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.4202 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 962 Z= 0.163 Angle : 0.456 3.138 1298 Z= 0.254 Chirality : 0.049 0.114 170 Planarity : 0.002 0.013 162 Dihedral : 4.398 9.575 140 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 6.38 % Allowed : 21.28 % Favored : 72.34 % 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: -3.71 (0.59), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.45), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR B 39 PHE 0.014 0.004 PHE A 94 HIS 0.003 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 962) covalent geometry : angle 0.45643 ( 1298) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.036 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 28 average time/residue: 0.4206 time to fit residues: 11.9488 Evaluate side-chains 30 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 10 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- 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 = 0.4544 r_free = 0.4544 target = 0.209335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.195722 restraints weight = 829.063| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 1.81 r_work: 0.4287 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4200 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 962 Z= 0.268 Angle : 0.541 3.142 1298 Z= 0.305 Chirality : 0.052 0.120 170 Planarity : 0.003 0.015 162 Dihedral : 5.238 13.394 140 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 6.38 % Allowed : 21.28 % Favored : 72.34 % 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: -3.92 (0.56), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.43), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR B 39 PHE 0.020 0.006 PHE B 94 HIS 0.004 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00571 ( 962) covalent geometry : angle 0.54059 ( 1298) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.040 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 30 average time/residue: 0.3977 time to fit residues: 12.1201 Evaluate side-chains 32 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 0 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 2 optimal weight: 0.0170 chunk 3 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- 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 = 0.4579 r_free = 0.4579 target = 0.213158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.199568 restraints weight = 860.678| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 1.89 r_work: 0.4337 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4248 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.009 962 Z= 0.079 Angle : 0.370 2.694 1298 Z= 0.208 Chirality : 0.049 0.118 170 Planarity : 0.002 0.010 162 Dihedral : 3.604 8.321 140 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 6.38 % Allowed : 21.28 % Favored : 72.34 % 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: -3.75 (0.60), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.46), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR A 39 PHE 0.016 0.004 PHE B 94 HIS 0.001 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00149 ( 962) covalent geometry : angle 0.37002 ( 1298) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.037 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 26 average time/residue: 0.3706 time to fit residues: 9.7922 Evaluate side-chains 26 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 12 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.0050 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 = 0.4572 r_free = 0.4572 target = 0.211132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.197434 restraints weight = 836.234| |-----------------------------------------------------------------------------| r_work (start): 0.4432 rms_B_bonded: 1.90 r_work: 0.4354 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4264 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 962 Z= 0.081 Angle : 0.364 2.849 1298 Z= 0.204 Chirality : 0.048 0.115 170 Planarity : 0.002 0.010 162 Dihedral : 3.505 7.591 140 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 5.32 % Allowed : 22.34 % Favored : 72.34 % 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: -3.70 (0.60), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.46), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR B 39 PHE 0.015 0.004 PHE B 94 HIS 0.001 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00160 ( 962) covalent geometry : angle 0.36388 ( 1298) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.034 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 27 average time/residue: 0.3521 time to fit residues: 9.6670 Evaluate side-chains 26 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 9 optimal weight: 0.0040 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 12 optimal weight: 0.0980 chunk 7 optimal weight: 4.9990 overall best weight: 1.6394 ------------------------------------------------------------------------------- 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 = 0.4575 r_free = 0.4575 target = 0.211675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.198154 restraints weight = 835.259| |-----------------------------------------------------------------------------| r_work (start): 0.4418 rms_B_bonded: 1.86 r_work: 0.4338 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4247 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 962 Z= 0.135 Angle : 0.418 2.923 1298 Z= 0.233 Chirality : 0.049 0.114 170 Planarity : 0.002 0.012 162 Dihedral : 4.193 9.270 140 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.26 % Allowed : 23.40 % Favored : 72.34 % 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: -3.69 (0.60), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.46), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 39 PHE 0.016 0.005 PHE B 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 962) covalent geometry : angle 0.41814 ( 1298) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.031 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 24 average time/residue: 0.3813 time to fit residues: 9.3029 Evaluate side-chains 26 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 12 optimal weight: 0.2980 chunk 8 optimal weight: 0.0270 chunk 6 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.2842 ------------------------------------------------------------------------------- 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 = 0.4532 r_free = 0.4532 target = 0.207230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.193642 restraints weight = 865.869| |-----------------------------------------------------------------------------| r_work (start): 0.4407 rms_B_bonded: 1.89 r_work: 0.4329 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4234 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 962 Z= 0.112 Angle : 0.398 2.881 1298 Z= 0.223 Chirality : 0.048 0.116 170 Planarity : 0.002 0.011 162 Dihedral : 3.997 8.929 140 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.26 % Allowed : 23.40 % Favored : 72.34 % 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: -3.67 (0.60), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.46), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR B 39 PHE 0.016 0.005 PHE A 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 962) covalent geometry : angle 0.39783 ( 1298) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.039 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 25 average time/residue: 0.3199 time to fit residues: 8.1657 Evaluate side-chains 27 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.4578 r_free = 0.4578 target = 0.212829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.199362 restraints weight = 848.990| |-----------------------------------------------------------------------------| r_work (start): 0.4415 rms_B_bonded: 1.85 r_work: 0.4334 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4243 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 962 Z= 0.132 Angle : 0.416 2.935 1298 Z= 0.233 Chirality : 0.049 0.115 170 Planarity : 0.002 0.011 162 Dihedral : 4.210 9.581 140 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 4.26 % Allowed : 23.40 % Favored : 72.34 % 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: -3.58 (0.60), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.46), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR A 39 PHE 0.017 0.005 PHE B 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 962) covalent geometry : angle 0.41585 ( 1298) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 760.80 seconds wall clock time: 14 minutes 9.98 seconds (849.98 seconds total)