Starting phenix.real_space_refine on Thu Sep 10 20:19:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pzd_72067/09_2026/9pzd_72067.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pzd_72067/09_2026/9pzd_72067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pzd_72067/09_2026/9pzd_72067.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pzd_72067/09_2026/9pzd_72067.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pzd_72067/09_2026/9pzd_72067.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pzd_72067/09_2026/9pzd_72067.map" } resolution = 3.3 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= 0.001 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 1680 2.51 5 N 610 2.21 5 O 480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2770 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 277 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "B" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 277 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "C" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 277 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "D" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 277 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "E" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 277 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "F" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 277 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "G" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 277 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "H" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 277 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "I" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 277 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "J" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 277 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Time building chain proxies: 0.53, per 1000 atoms: 0.19 Number of scatterers: 2770 At special positions: 0 Unit cell: (57.096, 98.28, 39.312, 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 480 8.00 N 610 7.00 C 1680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.12 Conformation dependent library (CDL) restraints added in 80.3 milliseconds 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 620 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 6.569A pdb=" N GLN A 5 " --> pdb=" O GLN C 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.968A pdb=" N HIS A 11 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N HIS C 11 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N HIS E 11 " --> pdb=" O LEU G 12 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N HIS G 11 " --> pdb=" O LEU I 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.511A pdb=" N HIS A 26 " --> pdb=" O GLN C 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 4 removed outlier: 6.243A pdb=" N HIS B 3 " --> pdb=" O GLN D 4 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N HIS D 3 " --> pdb=" O GLN F 4 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N HIS F 3 " --> pdb=" O GLN H 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 12 removed outlier: 8.807A pdb=" N LEU H 12 " --> pdb=" O GLN F 9 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N HIS F 11 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N HIS H 11 " --> pdb=" O LEU J 12 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 26 through 27 removed outlier: 6.158A pdb=" N HIS B 26 " --> pdb=" O GLN D 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 7 through 8 Processing sheet with id=AA8, first strand: chain 'E' and resid 22 through 23 removed outlier: 6.127A pdb=" N GLN E 22 " --> pdb=" O PHE G 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 26 through 27 removed outlier: 6.476A pdb=" N HIS F 26 " --> pdb=" O GLN H 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 27 through 30 10 hydrogen bonds defined for protein. 30 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.21 Time building geometry restraints manager: 0.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 470 1.29 - 1.35: 670 1.35 - 1.42: 210 1.42 - 1.49: 310 1.49 - 1.55: 1180 Bond restraints: 2840 Sorted by residual: bond pdb=" CB VAL E 21 " pdb=" CG1 VAL E 21 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.75e-01 bond pdb=" CB VAL C 21 " pdb=" CG1 VAL C 21 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.69e-01 bond pdb=" CB VAL G 21 " pdb=" CG1 VAL G 21 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.34e-01 bond pdb=" CB VAL H 21 " pdb=" CG1 VAL H 21 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.27e-01 bond pdb=" CB VAL I 21 " pdb=" CG1 VAL I 21 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.80e-01 ... (remaining 2835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 3705 2.25 - 4.50: 98 4.50 - 6.75: 5 6.75 - 9.00: 7 9.00 - 11.24: 5 Bond angle restraints: 3820 Sorted by residual: angle pdb=" CA LEU H 30 " pdb=" CB LEU H 30 " pdb=" CG LEU H 30 " ideal model delta sigma weight residual 116.30 127.54 -11.24 3.50e+00 8.16e-02 1.03e+01 angle pdb=" CA LEU B 30 " pdb=" CB LEU B 30 " pdb=" CG LEU B 30 " ideal model delta sigma weight residual 116.30 127.45 -11.15 3.50e+00 8.16e-02 1.01e+01 angle pdb=" CA LEU J 30 " pdb=" CB LEU J 30 " pdb=" CG LEU J 30 " ideal model delta sigma weight residual 116.30 127.45 -11.15 3.50e+00 8.16e-02 1.01e+01 angle pdb=" CA LEU F 30 " pdb=" CB LEU F 30 " pdb=" CG LEU F 30 " ideal model delta sigma weight residual 116.30 126.90 -10.60 3.50e+00 8.16e-02 9.18e+00 angle pdb=" CA LEU D 30 " pdb=" CB LEU D 30 " pdb=" CG LEU D 30 " ideal model delta sigma weight residual 116.30 126.89 -10.59 3.50e+00 8.16e-02 9.15e+00 ... (remaining 3815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1417 17.95 - 35.90: 193 35.90 - 53.86: 14 53.86 - 71.81: 41 71.81 - 89.76: 5 Dihedral angle restraints: 1670 sinusoidal: 750 harmonic: 920 Sorted by residual: dihedral pdb=" CA HIS I 24 " pdb=" C HIS I 24 " pdb=" N GLN I 25 " pdb=" CA GLN I 25 " ideal model delta harmonic sigma weight residual 180.00 156.66 23.34 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA HIS A 24 " pdb=" C HIS A 24 " pdb=" N GLN A 25 " pdb=" CA GLN A 25 " ideal model delta harmonic sigma weight residual 180.00 156.68 23.32 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA HIS A 3 " pdb=" C HIS A 3 " pdb=" N GLN A 4 " pdb=" CA GLN A 4 " ideal model delta harmonic sigma weight residual -180.00 -158.80 -21.20 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 1667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 156 0.027 - 0.055: 92 0.055 - 0.082: 79 0.082 - 0.109: 33 0.109 - 0.136: 10 Chirality restraints: 370 Sorted by residual: chirality pdb=" CA VAL B 15 " pdb=" N VAL B 15 " pdb=" C VAL B 15 " pdb=" CB VAL B 15 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA VAL J 15 " pdb=" N VAL J 15 " pdb=" C VAL J 15 " pdb=" CB VAL J 15 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA VAL A 15 " pdb=" N VAL A 15 " pdb=" C VAL A 15 " pdb=" CB VAL A 15 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 367 not shown) Planarity restraints: 540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS H 3 " -0.006 2.00e-02 2.50e+03 8.23e-03 1.02e+00 pdb=" CG HIS H 3 " 0.017 2.00e-02 2.50e+03 pdb=" ND1 HIS H 3 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS H 3 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS H 3 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS H 3 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 3 " 0.007 2.00e-02 2.50e+03 8.15e-03 9.96e-01 pdb=" CG HIS A 3 " -0.017 2.00e-02 2.50e+03 pdb=" ND1 HIS A 3 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 HIS A 3 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS A 3 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 3 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS I 3 " 0.006 2.00e-02 2.50e+03 7.99e-03 9.57e-01 pdb=" CG HIS I 3 " -0.017 2.00e-02 2.50e+03 pdb=" ND1 HIS I 3 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 HIS I 3 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS I 3 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS I 3 " 0.001 2.00e-02 2.50e+03 ... (remaining 537 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 253 2.75 - 3.29: 2708 3.29 - 3.82: 4243 3.82 - 4.36: 5173 4.36 - 4.90: 10178 Nonbonded interactions: 22555 Sorted by model distance: nonbonded pdb=" OE1 GLN A 4 " pdb=" NE2 GLN C 29 " model vdw 2.210 3.120 nonbonded pdb=" NE2 GLN D 10 " pdb=" OE1 GLN F 25 " model vdw 2.228 3.120 nonbonded pdb=" NE2 GLN B 10 " pdb=" OE1 GLN D 25 " model vdw 2.302 3.120 nonbonded pdb=" O GLN J 25 " pdb=" ND1 HIS J 26 " model vdw 2.310 3.120 nonbonded pdb=" O GLN B 25 " pdb=" ND1 HIS B 26 " model vdw 2.310 3.120 ... (remaining 22550 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.860 Find NCS groups from input model: 0.040 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:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 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 : 0.004 0.033 2840 Z= 0.172 Angle : 1.015 11.244 3820 Z= 0.501 Chirality : 0.053 0.136 370 Planarity : 0.003 0.008 540 Dihedral : 19.425 89.761 1050 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 23.55 % Favored : 76.45 % 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: -5.02 (0.28), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.21), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE E 23 HIS 0.010 0.003 HIS H 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 2840) covalent geometry : angle 1.01481 / 0.50 ( 3820) hydrogen bonds : bond 0.25944 / 13.67 ( 10) hydrogen bonds : angle 10.70661 / 6.80 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.059 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0241 time to fit residues: 0.1372 Evaluate side-chains 0 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 7 HIS J 9 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7381 r_free = 0.7381 target = 0.654788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 159)---------------| | r_work = 0.8068 r_free = 0.8068 target = 0.529779 restraints weight = 3955.577| |-----------------------------------------------------------------------------| r_work (start): 0.7389 rms_B_bonded: 1.71 r_work: 0.8146 rms_B_bonded: 0.06 restraints_weight: 0.5000 r_work: 0.8158 rms_B_bonded: 0.09 restraints_weight: 0.2500 r_work: 0.8099 rms_B_bonded: 0.95 restraints_weight: 0.1250 r_work (final): 0.8099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 2840 Z= 0.291 Angle : 1.094 9.695 3820 Z= 0.593 Chirality : 0.059 0.133 370 Planarity : 0.006 0.016 540 Dihedral : 9.966 29.655 300 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.55 % Favored : 83.45 % Rotamer: Outliers : 5.81 % Allowed : 24.84 % Favored : 69.35 % 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: -5.53 (0.28), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.21 (0.22), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.004 PHE D 23 HIS 0.017 0.006 HIS I 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.29 ( 2840) covalent geometry : angle 1.09425 / 0.59 ( 3820) hydrogen bonds : bond 0.03643 / 1.81 ( 10) hydrogen bonds : angle 7.40503 / 4.88 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 6 time to evaluate : 0.082 Fit side-chains REVERT: C 14 HIS cc_start: 0.6541 (OUTLIER) cc_final: 0.6264 (t-170) REVERT: D 14 HIS cc_start: 0.6386 (OUTLIER) cc_final: 0.6120 (t-170) REVERT: D 21 VAL cc_start: 0.7276 (OUTLIER) cc_final: 0.6939 (t) REVERT: E 14 HIS cc_start: 0.6403 (OUTLIER) cc_final: 0.6197 (t-170) REVERT: E 21 VAL cc_start: 0.7203 (OUTLIER) cc_final: 0.6978 (t) REVERT: F 21 VAL cc_start: 0.7156 (OUTLIER) cc_final: 0.6719 (t) REVERT: G 21 VAL cc_start: 0.7527 (OUTLIER) cc_final: 0.7321 (t) REVERT: H 21 VAL cc_start: 0.7367 (OUTLIER) cc_final: 0.7088 (t) REVERT: J 7 HIS cc_start: 0.6360 (OUTLIER) cc_final: 0.5529 (m-70) outliers start: 18 outliers final: 2 residues processed: 24 average time/residue: 0.0199 time to fit residues: 0.7987 Evaluate side-chains 12 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 1 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 HIS Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain E residue 14 HIS Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain J residue 7 HIS Chi-restraints excluded: chain J residue 21 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 HIS ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 HIS B 7 HIS B 14 HIS ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 HIS C 9 GLN F 14 HIS G 14 HIS H 7 HIS H 14 HIS I 7 HIS ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN I 14 HIS J 7 HIS J 14 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7343 r_free = 0.7343 target = 0.654477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 176)---------------| | r_work = 0.8054 r_free = 0.8054 target = 0.532689 restraints weight = 3960.860| |-----------------------------------------------------------------------------| r_work (start): 0.7343 rms_B_bonded: 0.98 r_work: 0.8167 rms_B_bonded: 0.02 restraints_weight: 0.5000 r_work: 0.8176 rms_B_bonded: 0.04 restraints_weight: 0.2500 r_work: 0.8170 rms_B_bonded: 0.16 restraints_weight: 0.1250 r_work: 0.8096 rms_B_bonded: 1.92 restraints_weight: 0.0625 r_work (final): 0.8096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2840 Z= 0.179 Angle : 0.888 8.484 3820 Z= 0.471 Chirality : 0.054 0.132 370 Planarity : 0.003 0.010 540 Dihedral : 8.989 28.578 300 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 5.16 % Allowed : 31.94 % Favored : 62.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.33 (0.30), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.23), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE D 23 HIS 0.011 0.003 HIS I 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 ( 2840) covalent geometry : angle 0.88783 / 0.47 ( 3820) hydrogen bonds : bond 0.02508 / 1.30 ( 10) hydrogen bonds : angle 6.69812 / 4.49 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 0 time to evaluate : 0.078 Fit side-chains REVERT: F 21 VAL cc_start: 0.7172 (OUTLIER) cc_final: 0.6878 (t) REVERT: H 7 HIS cc_start: 0.6753 (OUTLIER) cc_final: 0.6320 (m90) REVERT: I 7 HIS cc_start: 0.5941 (OUTLIER) cc_final: 0.5365 (m-70) outliers start: 16 outliers final: 6 residues processed: 16 average time/residue: 0.0215 time to fit residues: 0.5849 Evaluate side-chains 9 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 0 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 HIS Chi-restraints excluded: chain B residue 7 HIS Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain J residue 7 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 HIS ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 HIS ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 HIS ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 HIS H 14 HIS ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 7 HIS J 14 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7329 r_free = 0.7329 target = 0.650399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 135)---------------| | r_work = 0.8033 r_free = 0.8033 target = 0.527809 restraints weight = 3902.639| |-----------------------------------------------------------------------------| r_work (start): 0.7327 rms_B_bonded: 0.98 r_work: 0.8160 rms_B_bonded: 0.02 restraints_weight: 0.5000 r_work: 0.8171 rms_B_bonded: 0.03 restraints_weight: 0.2500 r_work: 0.8168 rms_B_bonded: 0.10 restraints_weight: 0.1250 r_work: 0.8103 rms_B_bonded: 1.60 restraints_weight: 0.0625 r_work (final): 0.8103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2840 Z= 0.190 Angle : 0.915 8.479 3820 Z= 0.477 Chirality : 0.054 0.155 370 Planarity : 0.003 0.010 540 Dihedral : 8.802 28.128 300 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.21 % Favored : 83.79 % Rotamer: Outliers : 5.16 % Allowed : 34.19 % Favored : 60.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.40 (0.31), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.24), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE D 23 HIS 0.010 0.003 HIS E 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 ( 2840) covalent geometry : angle 0.91473 / 0.48 ( 3820) hydrogen bonds : bond 0.02563 / 1.35 ( 10) hydrogen bonds : angle 6.56689 / 4.40 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 0 time to evaluate : 0.124 Fit side-chains REVERT: E 21 VAL cc_start: 0.7199 (OUTLIER) cc_final: 0.6932 (t) REVERT: H 7 HIS cc_start: 0.6580 (OUTLIER) cc_final: 0.6253 (m90) REVERT: H 30 LEU cc_start: 0.5397 (OUTLIER) cc_final: 0.5055 (tt) REVERT: J 7 HIS cc_start: 0.6176 (OUTLIER) cc_final: 0.5313 (m-70) outliers start: 16 outliers final: 7 residues processed: 16 average time/residue: 0.0276 time to fit residues: 0.7396 Evaluate side-chains 11 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 0 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 HIS Chi-restraints excluded: chain B residue 7 HIS Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain J residue 7 HIS Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 21 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 11 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 HIS ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 9 GLN B 7 HIS B 9 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 HIS ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 HIS H 14 HIS I 7 HIS ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7328 r_free = 0.7328 target = 0.650974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.8050 r_free = 0.8050 target = 0.523947 restraints weight = 3899.768| |-----------------------------------------------------------------------------| r_work (start): 0.7327 rms_B_bonded: 0.97 r_work: 0.8172 rms_B_bonded: 0.03 restraints_weight: 0.5000 r_work: 0.8182 rms_B_bonded: 0.04 restraints_weight: 0.2500 r_work: 0.8158 rms_B_bonded: 0.36 restraints_weight: 0.1250 r_work: 0.8039 rms_B_bonded: 3.32 restraints_weight: 0.0625 r_work (final): 0.8039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2840 Z= 0.194 Angle : 0.906 9.016 3820 Z= 0.474 Chirality : 0.054 0.151 370 Planarity : 0.003 0.010 540 Dihedral : 8.754 28.258 300 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.48 % Favored : 85.52 % Rotamer: Outliers : 9.03 % Allowed : 29.35 % Favored : 61.61 % 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: -5.43 (0.32), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.13 (0.24), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.003 PHE D 23 HIS 0.011 0.003 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 ( 2840) covalent geometry : angle 0.90604 / 0.47 ( 3820) hydrogen bonds : bond 0.02529 / 1.28 ( 10) hydrogen bonds : angle 6.48024 / 4.32 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 1 time to evaluate : 0.083 Fit side-chains REVERT: A 20 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6704 (tt0) REVERT: B 20 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6465 (tt0) REVERT: C 20 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6539 (tt0) REVERT: D 20 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6574 (tt0) REVERT: D 26 HIS cc_start: 0.6863 (OUTLIER) cc_final: 0.5170 (m-70) REVERT: E 20 GLN cc_start: 0.6971 (OUTLIER) cc_final: 0.6186 (tt0) REVERT: E 21 VAL cc_start: 0.7406 (OUTLIER) cc_final: 0.6939 (t) REVERT: F 20 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6350 (tt0) REVERT: G 20 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6586 (tt0) REVERT: H 7 HIS cc_start: 0.6566 (OUTLIER) cc_final: 0.6175 (m90) REVERT: H 20 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6645 (tt0) REVERT: I 7 HIS cc_start: 0.6179 (OUTLIER) cc_final: 0.5588 (m-70) REVERT: I 20 GLN cc_start: 0.6372 (OUTLIER) cc_final: 0.5776 (tt0) outliers start: 28 outliers final: 7 residues processed: 29 average time/residue: 0.0293 time to fit residues: 1.2792 Evaluate side-chains 21 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 1 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 HIS Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain B residue 7 HIS Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain E residue 20 GLN Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain F residue 20 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 21 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.0670 chunk 25 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 HIS ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 HIS ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 HIS ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 HIS D 14 HIS ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 HIS ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 HIS ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 7 HIS J 14 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7328 r_free = 0.7328 target = 0.656094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 125)---------------| | r_work = 0.8042 r_free = 0.8042 target = 0.529670 restraints weight = 3987.733| |-----------------------------------------------------------------------------| r_work (start): 0.7323 rms_B_bonded: 1.00 r_work: 0.8204 rms_B_bonded: 0.03 restraints_weight: 0.5000 r_work: 0.8215 rms_B_bonded: 0.04 restraints_weight: 0.2500 r_work: 0.8164 rms_B_bonded: 0.67 restraints_weight: 0.1250 r_work: 0.8064 rms_B_bonded: 3.44 restraints_weight: 0.0625 r_work (final): 0.8064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2840 Z= 0.146 Angle : 0.831 10.417 3820 Z= 0.423 Chirality : 0.052 0.151 370 Planarity : 0.002 0.008 540 Dihedral : 8.316 27.194 300 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 6.45 % Allowed : 32.26 % Favored : 61.29 % 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: -5.09 (0.33), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.25), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE F 23 HIS 0.007 0.002 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 2840) covalent geometry : angle 0.83131 / 0.42 ( 3820) hydrogen bonds : bond 0.02065 / 1.09 ( 10) hydrogen bonds : angle 6.02591 / 4.05 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 1 time to evaluate : 0.097 Fit side-chains REVERT: A 20 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6644 (tt0) REVERT: C 20 GLN cc_start: 0.6901 (OUTLIER) cc_final: 0.6435 (tt0) REVERT: D 14 HIS cc_start: 0.6417 (OUTLIER) cc_final: 0.5805 (t-90) REVERT: D 20 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6548 (tt0) REVERT: G 20 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6567 (tt0) REVERT: H 7 HIS cc_start: 0.6591 (OUTLIER) cc_final: 0.6176 (m90) REVERT: H 20 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.6531 (tt0) REVERT: J 7 HIS cc_start: 0.6090 (OUTLIER) cc_final: 0.5179 (m-70) outliers start: 20 outliers final: 9 residues processed: 20 average time/residue: 0.0341 time to fit residues: 1.0746 Evaluate side-chains 18 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 1 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 HIS Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain B residue 7 HIS Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain J residue 7 HIS Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 21 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 HIS ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 HIS ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 HIS ** C 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 HIS D 14 HIS ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 HIS ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 HIS ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7319 r_free = 0.7319 target = 0.648205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.8042 r_free = 0.8042 target = 0.520505 restraints weight = 3907.111| |-----------------------------------------------------------------------------| r_work (start): 0.7316 rms_B_bonded: 1.01 r_work: 0.8174 rms_B_bonded: 0.03 restraints_weight: 0.5000 r_work: 0.8184 rms_B_bonded: 0.04 restraints_weight: 0.2500 r_work: 0.8178 rms_B_bonded: 0.16 restraints_weight: 0.1250 r_work: 0.8085 rms_B_bonded: 2.27 restraints_weight: 0.0625 r_work (final): 0.8085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2840 Z= 0.195 Angle : 0.868 9.274 3820 Z= 0.455 Chirality : 0.053 0.148 370 Planarity : 0.003 0.010 540 Dihedral : 8.519 27.788 300 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.97 % Favored : 81.03 % Rotamer: Outliers : 11.61 % Allowed : 28.06 % Favored : 60.32 % 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: -5.33 (0.32), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.24), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.003 PHE F 23 HIS 0.011 0.002 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 2840) covalent geometry : angle 0.86818 / 0.45 ( 3820) hydrogen bonds : bond 0.02477 / 1.25 ( 10) hydrogen bonds : angle 6.15887 / 4.13 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 0 time to evaluate : 0.069 Fit side-chains REVERT: A 20 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6668 (tt0) REVERT: A 26 HIS cc_start: 0.6524 (OUTLIER) cc_final: 0.5279 (m-70) REVERT: B 20 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6439 (tt0) REVERT: B 26 HIS cc_start: 0.6635 (OUTLIER) cc_final: 0.5204 (m-70) REVERT: C 20 GLN cc_start: 0.6921 (OUTLIER) cc_final: 0.6420 (tt0) REVERT: C 26 HIS cc_start: 0.7079 (OUTLIER) cc_final: 0.5444 (m-70) REVERT: D 14 HIS cc_start: 0.6500 (OUTLIER) cc_final: 0.5923 (t-90) REVERT: D 20 GLN cc_start: 0.6826 (OUTLIER) cc_final: 0.6369 (tt0) REVERT: D 26 HIS cc_start: 0.6818 (OUTLIER) cc_final: 0.4877 (m-70) REVERT: D 30 LEU cc_start: 0.5790 (OUTLIER) cc_final: 0.5084 (tt) REVERT: E 20 GLN cc_start: 0.6957 (OUTLIER) cc_final: 0.6191 (tt0) REVERT: F 20 GLN cc_start: 0.6807 (OUTLIER) cc_final: 0.6138 (tt0) REVERT: F 30 LEU cc_start: 0.6018 (OUTLIER) cc_final: 0.5225 (tt) REVERT: G 20 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.6557 (tt0) REVERT: H 7 HIS cc_start: 0.6564 (OUTLIER) cc_final: 0.6113 (m90) REVERT: H 20 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6698 (tt0) REVERT: I 7 HIS cc_start: 0.6267 (OUTLIER) cc_final: 0.5665 (m-70) REVERT: I 20 GLN cc_start: 0.6184 (OUTLIER) cc_final: 0.5656 (tt0) outliers start: 36 outliers final: 10 residues processed: 36 average time/residue: 0.0311 time to fit residues: 1.5533 Evaluate side-chains 28 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 0 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 HIS Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain B residue 7 HIS Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain E residue 20 GLN Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain F residue 20 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 30 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 HIS ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 HIS ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 HIS ** C 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 HIS D 14 HIS ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 HIS ** H 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 HIS ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7276 r_free = 0.7276 target = 0.636417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 123)---------------| | r_work = 0.7938 r_free = 0.7938 target = 0.508476 restraints weight = 3946.318| |-----------------------------------------------------------------------------| r_work (start): 0.7261 rms_B_bonded: 1.02 r_work: 0.8107 rms_B_bonded: 0.04 restraints_weight: 0.5000 r_work: 0.8118 rms_B_bonded: 0.05 restraints_weight: 0.2500 r_work: 0.8110 rms_B_bonded: 0.20 restraints_weight: 0.1250 r_work: 0.7984 rms_B_bonded: 2.92 restraints_weight: 0.0625 r_work (final): 0.7984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 2840 Z= 0.271 Angle : 1.060 8.987 3820 Z= 0.568 Chirality : 0.057 0.153 370 Planarity : 0.005 0.014 540 Dihedral : 9.046 28.825 300 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 23.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.07 % Favored : 77.93 % Rotamer: Outliers : 10.00 % Allowed : 28.71 % Favored : 61.29 % 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: -5.65 (0.34), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.30 (0.26), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.004 PHE F 23 HIS 0.015 0.003 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.27 ( 2840) covalent geometry : angle 1.05953 / 0.57 ( 3820) hydrogen bonds : bond 0.03150 / 1.53 ( 10) hydrogen bonds : angle 6.89355 / 4.54 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 1 time to evaluate : 0.116 Fit side-chains REVERT: A 20 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6728 (tt0) REVERT: A 26 HIS cc_start: 0.6655 (OUTLIER) cc_final: 0.5526 (m-70) REVERT: B 20 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.6668 (tt0) REVERT: B 26 HIS cc_start: 0.6809 (OUTLIER) cc_final: 0.5671 (m-70) REVERT: C 20 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6613 (tt0) REVERT: C 26 HIS cc_start: 0.7361 (OUTLIER) cc_final: 0.5765 (m-70) REVERT: D 14 HIS cc_start: 0.6865 (OUTLIER) cc_final: 0.6091 (t-90) REVERT: D 20 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.6637 (tt0) REVERT: D 26 HIS cc_start: 0.7235 (OUTLIER) cc_final: 0.5358 (m-70) REVERT: D 30 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5774 (tt) REVERT: E 20 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6387 (tt0) REVERT: F 20 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.6294 (tt0) REVERT: F 26 HIS cc_start: 0.6663 (OUTLIER) cc_final: 0.5365 (m-70) REVERT: G 20 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6694 (tt0) REVERT: H 7 HIS cc_start: 0.6620 (OUTLIER) cc_final: 0.6227 (m90) REVERT: H 20 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.6885 (tt0) REVERT: I 7 HIS cc_start: 0.6352 (OUTLIER) cc_final: 0.5749 (m-70) REVERT: I 20 GLN cc_start: 0.6579 (OUTLIER) cc_final: 0.5950 (tt0) outliers start: 31 outliers final: 9 residues processed: 32 average time/residue: 0.0263 time to fit residues: 1.2001 Evaluate side-chains 28 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 1 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 HIS Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain B residue 7 HIS Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain E residue 20 GLN Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain F residue 20 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 21 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.0470 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 HIS B 7 HIS ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 HIS C 14 HIS D 7 HIS D 14 HIS ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 HIS ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 HIS ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7316 r_free = 0.7316 target = 0.655000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 122)---------------| | r_work = 0.7980 r_free = 0.7980 target = 0.525008 restraints weight = 4045.137| |-----------------------------------------------------------------------------| r_work (start): 0.7304 rms_B_bonded: 1.00 r_work: 0.8192 rms_B_bonded: 0.03 restraints_weight: 0.5000 r_work: 0.8201 rms_B_bonded: 0.06 restraints_weight: 0.2500 r_work: 0.8175 rms_B_bonded: 0.47 restraints_weight: 0.1250 r_work: 0.8025 rms_B_bonded: 4.15 restraints_weight: 0.0625 r_work (final): 0.8025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2840 Z= 0.151 Angle : 0.885 8.327 3820 Z= 0.458 Chirality : 0.053 0.148 370 Planarity : 0.002 0.008 540 Dihedral : 8.369 26.849 300 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 7.74 % Allowed : 30.65 % Favored : 61.61 % 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: -5.09 (0.34), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.26), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE F 23 HIS 0.006 0.001 HIS B 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 2840) covalent geometry : angle 0.88537 / 0.46 ( 3820) hydrogen bonds : bond 0.01918 / 1.03 ( 10) hydrogen bonds : angle 5.94909 / 3.97 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 0 time to evaluate : 0.098 Fit side-chains REVERT: A 20 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6667 (tt0) REVERT: B 20 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6551 (tt0) REVERT: C 20 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6461 (tt0) REVERT: D 14 HIS cc_start: 0.6794 (OUTLIER) cc_final: 0.6272 (t-90) REVERT: D 20 GLN cc_start: 0.6982 (OUTLIER) cc_final: 0.6466 (tt0) REVERT: D 30 LEU cc_start: 0.6015 (OUTLIER) cc_final: 0.5286 (tt) REVERT: E 20 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.6258 (tt0) REVERT: F 20 GLN cc_start: 0.6819 (OUTLIER) cc_final: 0.6136 (tt0) REVERT: F 30 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5228 (tt) REVERT: G 20 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6574 (tt0) REVERT: H 7 HIS cc_start: 0.6510 (OUTLIER) cc_final: 0.6001 (m90) REVERT: H 20 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6766 (tt0) REVERT: I 7 HIS cc_start: 0.6360 (OUTLIER) cc_final: 0.5914 (m90) REVERT: I 20 GLN cc_start: 0.6493 (OUTLIER) cc_final: 0.5923 (tt0) outliers start: 24 outliers final: 9 residues processed: 24 average time/residue: 0.0299 time to fit residues: 1.0844 Evaluate side-chains 23 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 0 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 HIS Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain B residue 7 HIS Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain E residue 20 GLN Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain F residue 20 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 21 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 HIS ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 HIS ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 HIS ** C 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 HIS D 14 HIS ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 HIS ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 HIS ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7315 r_free = 0.7315 target = 0.647557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 127)---------------| | r_work = 0.8036 r_free = 0.8036 target = 0.515349 restraints weight = 3949.502| |-----------------------------------------------------------------------------| r_work (start): 0.7309 rms_B_bonded: 0.99 r_work: 0.8206 rms_B_bonded: 0.03 restraints_weight: 0.5000 r_work: 0.8216 rms_B_bonded: 0.04 restraints_weight: 0.2500 r_work: 0.8210 rms_B_bonded: 0.15 restraints_weight: 0.1250 r_work: 0.8090 rms_B_bonded: 2.70 restraints_weight: 0.0625 r_work (final): 0.8090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2840 Z= 0.215 Angle : 0.960 8.349 3820 Z= 0.506 Chirality : 0.055 0.150 370 Planarity : 0.004 0.011 540 Dihedral : 8.619 27.788 300 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.41 % Favored : 77.59 % Rotamer: Outliers : 7.42 % Allowed : 30.97 % Favored : 61.61 % 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: -5.24 (0.36), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.28), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.003 PHE A 23 HIS 0.011 0.002 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.22 ( 2840) covalent geometry : angle 0.96016 / 0.51 ( 3820) hydrogen bonds : bond 0.02464 / 1.24 ( 10) hydrogen bonds : angle 6.33796 / 4.19 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 2 time to evaluate : 0.099 Fit side-chains REVERT: A 20 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6663 (tt0) REVERT: B 20 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6599 (tt0) REVERT: C 20 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6551 (tt0) REVERT: D 14 HIS cc_start: 0.6816 (OUTLIER) cc_final: 0.6056 (t-90) REVERT: D 20 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6517 (tt0) REVERT: D 30 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5410 (tt) REVERT: E 20 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6308 (tt0) REVERT: F 20 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.6081 (tt0) REVERT: F 30 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5308 (tt) REVERT: G 20 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6582 (tt0) REVERT: H 7 HIS cc_start: 0.6647 (OUTLIER) cc_final: 0.6203 (m90) REVERT: H 20 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6709 (tt0) REVERT: I 7 HIS cc_start: 0.6476 (OUTLIER) cc_final: 0.5836 (m-70) REVERT: I 20 GLN cc_start: 0.6395 (OUTLIER) cc_final: 0.5768 (tt0) outliers start: 23 outliers final: 9 residues processed: 24 average time/residue: 0.0349 time to fit residues: 1.2121 Evaluate side-chains 25 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 2 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 HIS Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain B residue 7 HIS Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain E residue 20 GLN Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain F residue 20 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 21 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 HIS ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 HIS C 7 HIS ** C 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 HIS ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 HIS ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 HIS ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7339 r_free = 0.7339 target = 0.652933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 127)---------------| | r_work = 0.8081 r_free = 0.8081 target = 0.523422 restraints weight = 3924.866| |-----------------------------------------------------------------------------| r_work (start): 0.7332 rms_B_bonded: 0.95 r_work: 0.8240 rms_B_bonded: 0.03 restraints_weight: 0.5000 r_work: 0.8252 rms_B_bonded: 0.03 restraints_weight: 0.2500 r_work: 0.8248 rms_B_bonded: 0.12 restraints_weight: 0.1250 r_work: 0.8168 rms_B_bonded: 1.89 restraints_weight: 0.0625 r_work (final): 0.8168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2840 Z= 0.159 Angle : 0.875 7.843 3820 Z= 0.453 Chirality : 0.053 0.146 370 Planarity : 0.003 0.008 540 Dihedral : 8.378 27.031 300 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 7.10 % Allowed : 30.97 % Favored : 61.94 % 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: -5.10 (0.35), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.26), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE F 23 HIS 0.007 0.002 HIS D 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 2840) covalent geometry : angle 0.87484 / 0.45 ( 3820) hydrogen bonds : bond 0.02064 / 1.10 ( 10) hydrogen bonds : angle 5.90144 / 3.93 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 914.34 seconds wall clock time: 16 minutes 19.40 seconds (979.40 seconds total)