Starting phenix.real_space_refine on Sat May 2 06:53:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9riw_54007/05_2026/9riw_54007.cif Found real_map, /net/cci-nas-00/data/ceres_data/9riw_54007/05_2026/9riw_54007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9riw_54007/05_2026/9riw_54007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9riw_54007/05_2026/9riw_54007.map" model { file = "/net/cci-nas-00/data/ceres_data/9riw_54007/05_2026/9riw_54007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9riw_54007/05_2026/9riw_54007.cif" } resolution = 3.1 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= 0.003 sd= 0.049 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: 5 Type Number sf(0) Gaussians S 8 5.16 5 C 968 2.51 5 N 240 2.21 5 O 264 1.98 5 H 1568 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3048 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 381 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "A" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 381 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 381 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "D" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 381 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "E" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 381 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "F" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 381 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "G" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 381 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "H" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 381 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Time building chain proxies: 0.74, per 1000 atoms: 0.24 Number of scatterers: 3048 At special positions: 0 Unit cell: (51.83, 86.62, 34.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 O 264 8.00 N 240 7.00 C 968 6.00 H 1568 1.00 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: 0.26 Conformation dependent library (CDL) restraints added in 78.1 milliseconds 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 336 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 22 removed outlier: 6.378A pdb=" N PHE B 19 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N GLU A 22 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA B 21 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 31 removed outlier: 6.658A pdb=" N ALA B 30 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA C 30 " --> pdb=" O ILE D 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.159A pdb=" N MET B 35 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N MET C 35 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 18 through 22 Processing sheet with id=AA5, first strand: chain 'E' and resid 30 through 31 removed outlier: 6.605A pdb=" N ALA E 30 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA F 30 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA G 30 " --> pdb=" O ILE H 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.108A pdb=" N MET E 35 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N MET F 35 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N MET G 35 " --> pdb=" O VAL H 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 22 hydrogen bonds defined for protein. 66 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.61 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 1568 1.03 - 1.22: 4 1.22 - 1.42: 569 1.42 - 1.61: 899 1.61 - 1.80: 16 Bond restraints: 3056 Sorted by residual: bond pdb=" N LEU A 34 " pdb=" CA LEU A 34 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.21e-02 6.83e+03 8.30e+00 bond pdb=" N LEU G 34 " pdb=" CA LEU G 34 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.20e-02 6.94e+03 8.19e+00 bond pdb=" N LEU C 34 " pdb=" CA LEU C 34 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.20e-02 6.94e+03 8.11e+00 bond pdb=" N LEU B 34 " pdb=" CA LEU B 34 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.21e-02 6.83e+03 8.10e+00 bond pdb=" N LEU F 34 " pdb=" CA LEU F 34 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.97e+00 ... (remaining 3051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 5341 1.29 - 2.57: 134 2.57 - 3.86: 57 3.86 - 5.15: 12 5.15 - 6.43: 8 Bond angle restraints: 5552 Sorted by residual: angle pdb=" N LEU C 34 " pdb=" CA LEU C 34 " pdb=" CB LEU C 34 " ideal model delta sigma weight residual 110.71 117.14 -6.43 1.66e+00 3.63e-01 1.50e+01 angle pdb=" N LEU G 34 " pdb=" CA LEU G 34 " pdb=" CB LEU G 34 " ideal model delta sigma weight residual 110.71 117.10 -6.39 1.66e+00 3.63e-01 1.48e+01 angle pdb=" N LEU B 34 " pdb=" CA LEU B 34 " pdb=" CB LEU B 34 " ideal model delta sigma weight residual 111.13 117.46 -6.33 1.81e+00 3.05e-01 1.22e+01 angle pdb=" N LEU F 34 " pdb=" CA LEU F 34 " pdb=" CB LEU F 34 " ideal model delta sigma weight residual 111.13 117.41 -6.28 1.81e+00 3.05e-01 1.21e+01 angle pdb=" N LEU H 34 " pdb=" CA LEU H 34 " pdb=" CB LEU H 34 " ideal model delta sigma weight residual 110.71 116.04 -5.33 1.66e+00 3.63e-01 1.03e+01 ... (remaining 5547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.84: 1090 12.84 - 25.69: 166 25.69 - 38.53: 56 38.53 - 51.37: 40 51.37 - 64.22: 32 Dihedral angle restraints: 1384 sinusoidal: 768 harmonic: 616 Sorted by residual: dihedral pdb=" N MET D 35 " pdb=" CA MET D 35 " pdb=" CB MET D 35 " pdb=" CG MET D 35 " ideal model delta sinusoidal sigma weight residual -60.00 -114.71 54.71 3 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" N MET F 35 " pdb=" CA MET F 35 " pdb=" CB MET F 35 " pdb=" CG MET F 35 " ideal model delta sinusoidal sigma weight residual -60.00 -114.66 54.66 3 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" N MET B 35 " pdb=" CA MET B 35 " pdb=" CB MET B 35 " pdb=" CG MET B 35 " ideal model delta sinusoidal sigma weight residual -60.00 -114.66 54.66 3 1.50e+01 4.44e-03 9.30e+00 ... (remaining 1381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 118 0.028 - 0.056: 64 0.056 - 0.084: 27 0.084 - 0.112: 23 0.112 - 0.140: 8 Chirality restraints: 240 Sorted by residual: chirality pdb=" CA ILE C 31 " pdb=" N ILE C 31 " pdb=" C ILE C 31 " pdb=" CB ILE C 31 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE D 31 " pdb=" N ILE D 31 " pdb=" C ILE D 31 " pdb=" CB ILE D 31 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE G 31 " pdb=" N ILE G 31 " pdb=" C ILE G 31 " pdb=" CB ILE G 31 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 237 not shown) Planarity restraints: 448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 33 " 0.005 2.00e-02 2.50e+03 1.08e-02 1.16e+00 pdb=" C GLY E 33 " -0.019 2.00e-02 2.50e+03 pdb=" O GLY E 33 " 0.007 2.00e-02 2.50e+03 pdb=" N LEU E 34 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 33 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.12e+00 pdb=" C GLY A 33 " 0.018 2.00e-02 2.50e+03 pdb=" O GLY A 33 " -0.007 2.00e-02 2.50e+03 pdb=" N LEU A 34 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 34 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" N MET D 35 " 0.017 2.00e-02 2.50e+03 pdb=" CA MET D 35 " -0.005 2.00e-02 2.50e+03 pdb=" H MET D 35 " -0.007 2.00e-02 2.50e+03 ... (remaining 445 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.43: 1638 2.43 - 2.97: 6934 2.97 - 3.51: 7524 3.51 - 4.06: 10940 4.06 - 4.60: 14933 Nonbonded interactions: 41969 Sorted by model distance: nonbonded pdb=" H GLY B 25 " pdb=" O VAL A 24 " model vdw 1.886 2.450 nonbonded pdb=" O VAL E 24 " pdb=" H GLY F 25 " model vdw 1.886 2.450 nonbonded pdb=" HB3 ALA D 21 " pdb="HD11 LEU H 34 " model vdw 1.895 2.440 nonbonded pdb=" O VAL G 24 " pdb=" H GLY H 25 " model vdw 1.898 2.450 nonbonded pdb=" O VAL C 24 " pdb=" H GLY D 25 " model vdw 1.899 2.450 ... (remaining 41964 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 5.000 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: 0.020 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.200 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 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 0.037 1488 Z= 0.346 Angle : 0.772 6.433 1984 Z= 0.450 Chirality : 0.052 0.140 240 Planarity : 0.003 0.011 248 Dihedral : 19.864 64.217 512 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.83 % Favored : 79.17 % Rotamer: Outliers : 0.00 % Allowed : 42.11 % Favored : 57.89 % 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 are not related in a simple way. whole: -4.00 (0.50), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE G 19 Details of bonding type rmsd covalent geometry : bond 0.00595 ( 1488) covalent geometry : angle 0.77177 ( 1984) hydrogen bonds : bond 0.14139 ( 22) hydrogen bonds : angle 7.93844 ( 66) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.081 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1636 time to fit residues: 7.2066 Evaluate side-chains 37 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN A 27 ASN C 27 ASN D 27 ASN E 27 ASN F 27 ASN G 27 ASN H 27 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.145453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.133179 restraints weight = 5996.476| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.96 r_work: 0.3809 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 1488 Z= 0.134 Angle : 0.439 2.410 1984 Z= 0.229 Chirality : 0.051 0.131 240 Planarity : 0.001 0.004 248 Dihedral : 4.081 12.057 200 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 0.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.15 % Favored : 83.85 % Rotamer: Outliers : 4.61 % Allowed : 41.45 % Favored : 53.95 % 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 are not related in a simple way. whole: -3.93 (0.49), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE E 19 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 1488) covalent geometry : angle 0.43858 ( 1984) hydrogen bonds : bond 0.02387 ( 22) hydrogen bonds : angle 4.29798 ( 66) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.078 Fit side-chains REVERT: A 17 LEU cc_start: 0.8213 (mp) cc_final: 0.8006 (mp) REVERT: F 23 ASP cc_start: 0.6861 (m-30) cc_final: 0.6503 (m-30) outliers start: 7 outliers final: 4 residues processed: 40 average time/residue: 0.1642 time to fit residues: 7.2046 Evaluate side-chains 43 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain F residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 2 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.135230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.123331 restraints weight = 5838.130| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.80 r_work: 0.3720 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 1488 Z= 0.241 Angle : 0.501 3.916 1984 Z= 0.261 Chirality : 0.048 0.127 240 Planarity : 0.002 0.008 248 Dihedral : 4.697 13.818 200 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 0.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 5.26 % Allowed : 39.47 % Favored : 55.26 % 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 are not related in a simple way. whole: -4.12 (0.47), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.36), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE D 19 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 1488) covalent geometry : angle 0.50079 ( 1984) hydrogen bonds : bond 0.02330 ( 22) hydrogen bonds : angle 4.03609 ( 66) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: F 23 ASP cc_start: 0.7367 (m-30) cc_final: 0.6950 (m-30) outliers start: 8 outliers final: 6 residues processed: 44 average time/residue: 0.1496 time to fit residues: 7.2719 Evaluate side-chains 47 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 13 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.131747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.119750 restraints weight = 5812.412| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.79 r_work: 0.3746 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1488 Z= 0.111 Angle : 0.413 3.684 1984 Z= 0.213 Chirality : 0.051 0.127 240 Planarity : 0.001 0.004 248 Dihedral : 4.398 13.550 200 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 5.92 % Allowed : 40.13 % Favored : 53.95 % 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 are not related in a simple way. whole: -4.10 (0.47), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.36), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE C 19 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 1488) covalent geometry : angle 0.41261 ( 1984) hydrogen bonds : bond 0.01437 ( 22) hydrogen bonds : angle 3.92176 ( 66) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.049 Fit side-chains REVERT: E 23 ASP cc_start: 0.7261 (m-30) cc_final: 0.6867 (t0) REVERT: F 23 ASP cc_start: 0.7316 (m-30) cc_final: 0.7028 (m-30) outliers start: 9 outliers final: 7 residues processed: 46 average time/residue: 0.1392 time to fit residues: 7.1083 Evaluate side-chains 48 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 31 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.128454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.116154 restraints weight = 5772.465| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.84 r_work: 0.3706 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1488 Z= 0.149 Angle : 0.429 3.930 1984 Z= 0.221 Chirality : 0.049 0.125 240 Planarity : 0.001 0.006 248 Dihedral : 4.481 13.339 200 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 0.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.02 % Favored : 86.98 % Rotamer: Outliers : 4.61 % Allowed : 42.11 % Favored : 53.29 % 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 are not related in a simple way. whole: -4.06 (0.47), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.36), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE B 19 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 1488) covalent geometry : angle 0.42912 ( 1984) hydrogen bonds : bond 0.01415 ( 22) hydrogen bonds : angle 3.93889 ( 66) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.081 Fit side-chains REVERT: E 23 ASP cc_start: 0.7216 (m-30) cc_final: 0.6893 (t0) REVERT: F 23 ASP cc_start: 0.7424 (m-30) cc_final: 0.7149 (m-30) outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 0.1464 time to fit residues: 7.2822 Evaluate side-chains 47 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain H residue 31 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 5 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.129917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.117608 restraints weight = 5842.502| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.85 r_work: 0.3725 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1488 Z= 0.095 Angle : 0.393 3.679 1984 Z= 0.202 Chirality : 0.051 0.127 240 Planarity : 0.001 0.004 248 Dihedral : 4.224 12.830 200 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 5.26 % Allowed : 43.42 % Favored : 51.32 % 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 are not related in a simple way. whole: -4.04 (0.46), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.35), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE B 19 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 1488) covalent geometry : angle 0.39348 ( 1984) hydrogen bonds : bond 0.01164 ( 22) hydrogen bonds : angle 3.85750 ( 66) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: E 23 ASP cc_start: 0.7237 (m-30) cc_final: 0.6821 (t0) REVERT: F 22 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6867 (tm-30) outliers start: 8 outliers final: 6 residues processed: 44 average time/residue: 0.1374 time to fit residues: 6.6887 Evaluate side-chains 47 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 31 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.125851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.113433 restraints weight = 5905.780| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.87 r_work: 0.3680 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 1488 Z= 0.201 Angle : 0.456 3.934 1984 Z= 0.237 Chirality : 0.048 0.122 240 Planarity : 0.001 0.008 248 Dihedral : 4.746 14.132 200 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 4.61 % Allowed : 43.42 % Favored : 51.97 % 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 are not related in a simple way. whole: -4.12 (0.46), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.35), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE B 19 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 1488) covalent geometry : angle 0.45648 ( 1984) hydrogen bonds : bond 0.01522 ( 22) hydrogen bonds : angle 4.07848 ( 66) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: E 23 ASP cc_start: 0.7243 (m-30) cc_final: 0.6897 (t0) REVERT: F 22 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6897 (tm-30) outliers start: 7 outliers final: 6 residues processed: 44 average time/residue: 0.1339 time to fit residues: 6.5540 Evaluate side-chains 47 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 31 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.126078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.113746 restraints weight = 5901.979| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.83 r_work: 0.3679 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 1488 Z= 0.208 Angle : 0.465 4.030 1984 Z= 0.240 Chirality : 0.048 0.123 240 Planarity : 0.001 0.010 248 Dihedral : 4.866 14.493 200 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 5.26 % Allowed : 42.76 % Favored : 51.97 % 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 are not related in a simple way. whole: -4.22 (0.45), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.34), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE D 19 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 1488) covalent geometry : angle 0.46507 ( 1984) hydrogen bonds : bond 0.01524 ( 22) hydrogen bonds : angle 4.19502 ( 66) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: E 23 ASP cc_start: 0.7306 (m-30) cc_final: 0.6955 (t0) REVERT: F 22 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6905 (tm-30) outliers start: 8 outliers final: 7 residues processed: 46 average time/residue: 0.1383 time to fit residues: 7.0863 Evaluate side-chains 50 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 31 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.0010 chunk 2 optimal weight: 0.0870 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 0.0570 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.3282 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.131498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.119540 restraints weight = 5945.632| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.82 r_work: 0.3766 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.014 1488 Z= 0.060 Angle : 0.378 3.725 1984 Z= 0.191 Chirality : 0.053 0.126 240 Planarity : 0.001 0.004 248 Dihedral : 3.987 12.592 200 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 3.29 % Allowed : 43.42 % Favored : 53.29 % 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 are not related in a simple way. whole: -4.07 (0.45), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.35), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.000 PHE E 19 Details of bonding type rmsd covalent geometry : bond 0.00124 ( 1488) covalent geometry : angle 0.37834 ( 1984) hydrogen bonds : bond 0.00931 ( 22) hydrogen bonds : angle 3.83372 ( 66) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: E 23 ASP cc_start: 0.7320 (m-30) cc_final: 0.7034 (t0) REVERT: F 22 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6767 (tm-30) outliers start: 5 outliers final: 3 residues processed: 40 average time/residue: 0.1377 time to fit residues: 6.0707 Evaluate side-chains 42 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain H residue 31 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 0.0470 chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.129398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.117612 restraints weight = 5777.978| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.76 r_work: 0.3743 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1488 Z= 0.092 Angle : 0.390 3.908 1984 Z= 0.198 Chirality : 0.051 0.127 240 Planarity : 0.001 0.006 248 Dihedral : 4.071 12.663 200 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 2.63 % Allowed : 44.08 % Favored : 53.29 % 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 are not related in a simple way. whole: -4.01 (0.46), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.35), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE B 19 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 1488) covalent geometry : angle 0.39026 ( 1984) hydrogen bonds : bond 0.01039 ( 22) hydrogen bonds : angle 3.77746 ( 66) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: E 23 ASP cc_start: 0.7307 (m-30) cc_final: 0.7001 (t0) REVERT: F 22 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6762 (tm-30) outliers start: 4 outliers final: 3 residues processed: 41 average time/residue: 0.1516 time to fit residues: 6.8457 Evaluate side-chains 43 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain H residue 31 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.125984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.113940 restraints weight = 5892.661| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.78 r_work: 0.3689 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 1488 Z= 0.177 Angle : 0.438 3.955 1984 Z= 0.225 Chirality : 0.049 0.122 240 Planarity : 0.001 0.009 248 Dihedral : 4.561 13.771 200 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 3.29 % Allowed : 44.08 % Favored : 52.63 % 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 are not related in a simple way. whole: -4.12 (0.46), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.35), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE C 19 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 1488) covalent geometry : angle 0.43759 ( 1984) hydrogen bonds : bond 0.01388 ( 22) hydrogen bonds : angle 3.95887 ( 66) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1592.94 seconds wall clock time: 27 minutes 43.87 seconds (1663.87 seconds total)