Starting phenix.real_space_refine on Fri Aug 22 12:38:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v1n_42886/08_2025/8v1n_42886.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v1n_42886/08_2025/8v1n_42886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v1n_42886/08_2025/8v1n_42886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v1n_42886/08_2025/8v1n_42886.map" model { file = "/net/cci-nas-00/data/ceres_data/8v1n_42886/08_2025/8v1n_42886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v1n_42886/08_2025/8v1n_42886.cif" } resolution = 3.0 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= 1.000 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 936 2.51 5 N 258 2.21 5 O 246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1440 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 128 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 112 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "C" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 128 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 112 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "E" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 128 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "F" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 112 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "G" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 128 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "H" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 112 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "I" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 128 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "J" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 112 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "K" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 128 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "L" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 112 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Time building chain proxies: 0.32, per 1000 atoms: 0.22 Number of scatterers: 1440 At special positions: 0 Unit cell: (73.416, 60.648, 31.92, 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 246 8.00 N 258 7.00 C 936 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.15 Conformation dependent library (CDL) restraints added in 34.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 312 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 6 removed outlier: 9.138A pdb=" N ILE A 3 " --> pdb=" O LYS E 4 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N VAL E 6 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N HIS A 5 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS A 4 " --> pdb=" O ILE I 3 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS I 5 " --> pdb=" O LYS A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.394A pdb=" N SER A 11 " --> pdb=" O VAL E 12 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 7 through 8 removed outlier: 6.649A pdb=" N LEU B 7 " --> pdb=" O GLY F 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 12 through 15 removed outlier: 6.634A pdb=" N VAL B 12 " --> pdb=" O GLN F 13 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N VAL F 15 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE B 14 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN B 13 " --> pdb=" O ILE J 14 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 3 through 6 removed outlier: 6.904A pdb=" N VAL C 6 " --> pdb=" O HIS G 5 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE C 3 " --> pdb=" O LYS K 4 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL K 6 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N HIS C 5 " --> pdb=" O VAL K 6 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.126A pdb=" N SER C 11 " --> pdb=" O VAL G 12 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 7 through 8 removed outlier: 6.728A pdb=" N LEU D 7 " --> pdb=" O GLY H 8 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 12 through 16 removed outlier: 6.588A pdb=" N GLN D 13 " --> pdb=" O ILE L 14 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N TYR L 16 " --> pdb=" O GLN D 13 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL D 15 " --> pdb=" O TYR L 16 " (cutoff:3.500A) 11 hydrogen bonds defined for protein. 33 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: 0.09 Time building geometry restraints manager: 0.18 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: 222 1.29 - 1.35: 222 1.35 - 1.42: 130 1.42 - 1.48: 194 1.48 - 1.55: 684 Bond restraints: 1452 Sorted by residual: bond pdb=" CA SER A 11 " pdb=" CB SER A 11 " ideal model delta sigma weight residual 1.535 1.492 0.042 2.02e-02 2.45e+03 4.39e+00 bond pdb=" N SER A 11 " pdb=" CA SER A 11 " ideal model delta sigma weight residual 1.455 1.481 -0.026 1.25e-02 6.40e+03 4.29e+00 bond pdb=" CB VAL A 12 " pdb=" CG1 VAL A 12 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.12e-01 bond pdb=" C SER A 11 " pdb=" O SER A 11 " ideal model delta sigma weight residual 1.234 1.242 -0.008 1.18e-02 7.18e+03 4.78e-01 bond pdb=" CB GLN G 13 " pdb=" CG GLN G 13 " ideal model delta sigma weight residual 1.520 1.540 -0.020 3.00e-02 1.11e+03 4.44e-01 ... (remaining 1447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 1786 1.29 - 2.57: 125 2.57 - 3.86: 11 3.86 - 5.15: 4 5.15 - 6.43: 6 Bond angle restraints: 1932 Sorted by residual: angle pdb=" CB GLN G 13 " pdb=" CG GLN G 13 " pdb=" CD GLN G 13 " ideal model delta sigma weight residual 112.60 117.15 -4.55 1.70e+00 3.46e-01 7.16e+00 angle pdb=" CA SER A 11 " pdb=" C SER A 11 " pdb=" O SER A 11 " ideal model delta sigma weight residual 120.60 118.16 2.44 1.20e+00 6.94e-01 4.15e+00 angle pdb=" N GLN A 13 " pdb=" CA GLN A 13 " pdb=" C GLN A 13 " ideal model delta sigma weight residual 112.13 114.73 -2.60 1.37e+00 5.33e-01 3.60e+00 angle pdb=" CA LEU L 7 " pdb=" CB LEU L 7 " pdb=" CG LEU L 7 " ideal model delta sigma weight residual 116.30 122.73 -6.43 3.50e+00 8.16e-02 3.38e+00 angle pdb=" CA LEU F 7 " pdb=" CB LEU F 7 " pdb=" CG LEU F 7 " ideal model delta sigma weight residual 116.30 122.73 -6.43 3.50e+00 8.16e-02 3.38e+00 ... (remaining 1927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 671 15.49 - 30.99: 88 30.99 - 46.48: 49 46.48 - 61.98: 18 61.98 - 77.47: 2 Dihedral angle restraints: 828 sinusoidal: 324 harmonic: 504 Sorted by residual: dihedral pdb=" N GLN K 13 " pdb=" CA GLN K 13 " pdb=" CB GLN K 13 " pdb=" CG GLN K 13 " ideal model delta sinusoidal sigma weight residual -60.00 -119.96 59.96 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CG LYS J 17 " pdb=" CD LYS J 17 " pdb=" CE LYS J 17 " pdb=" NZ LYS J 17 " ideal model delta sinusoidal sigma weight residual 180.00 122.96 57.04 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N GLN C 13 " pdb=" CA GLN C 13 " pdb=" CB GLN C 13 " pdb=" CG GLN C 13 " ideal model delta sinusoidal sigma weight residual -60.00 -114.07 54.07 3 1.50e+01 4.44e-03 9.25e+00 ... (remaining 825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 108 0.025 - 0.049: 48 0.049 - 0.074: 17 0.074 - 0.099: 25 0.099 - 0.124: 30 Chirality restraints: 228 Sorted by residual: chirality pdb=" CA ILE L 14 " pdb=" N ILE L 14 " pdb=" C ILE L 14 " pdb=" CB ILE L 14 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA VAL E 12 " pdb=" N VAL E 12 " pdb=" C VAL E 12 " pdb=" CB VAL E 12 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA VAL G 15 " pdb=" N VAL G 15 " pdb=" C VAL G 15 " pdb=" CB VAL G 15 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.29e-01 ... (remaining 225 not shown) Planarity restraints: 228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN G 13 " -0.005 2.00e-02 2.50e+03 1.05e-02 1.09e+00 pdb=" C GLN G 13 " 0.018 2.00e-02 2.50e+03 pdb=" O GLN G 13 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE G 14 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 10 " 0.003 2.00e-02 2.50e+03 7.11e-03 5.05e-01 pdb=" C GLY A 10 " -0.012 2.00e-02 2.50e+03 pdb=" O GLY A 10 " 0.005 2.00e-02 2.50e+03 pdb=" N SER A 11 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 3 " 0.003 2.00e-02 2.50e+03 5.99e-03 3.59e-01 pdb=" C ILE K 3 " -0.010 2.00e-02 2.50e+03 pdb=" O ILE K 3 " 0.004 2.00e-02 2.50e+03 pdb=" N LYS K 4 " 0.003 2.00e-02 2.50e+03 ... (remaining 225 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 219 2.77 - 3.30: 1321 3.30 - 3.83: 2181 3.83 - 4.37: 2321 4.37 - 4.90: 4901 Nonbonded interactions: 10943 Sorted by model distance: nonbonded pdb=" OG SER E 11 " pdb=" OE1 GLN F 13 " model vdw 2.237 3.040 nonbonded pdb=" OG SER I 11 " pdb=" OE1 GLN J 13 " model vdw 2.284 3.040 nonbonded pdb=" OG SER K 11 " pdb=" OE1 GLN L 13 " model vdw 2.330 3.040 nonbonded pdb=" OG SER G 11 " pdb=" NE2 GLN H 13 " model vdw 2.392 3.120 nonbonded pdb=" OE1 GLN E 13 " pdb=" NE2 GLN F 13 " model vdw 2.422 3.120 ... (remaining 10938 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' and resid 3 through 17) selection = chain 'B' selection = (chain 'C' and resid 3 through 17) selection = chain 'D' selection = (chain 'E' and resid 3 through 17) selection = chain 'F' selection = (chain 'G' and resid 3 through 17) selection = chain 'H' selection = (chain 'I' and resid 3 through 17) selection = chain 'J' selection = (chain 'K' and resid 3 through 17) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 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: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.230 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:4.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 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 0.042 1452 Z= 0.167 Angle : 0.758 6.433 1932 Z= 0.412 Chirality : 0.055 0.124 228 Planarity : 0.002 0.010 228 Dihedral : 19.550 77.474 516 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.21 % Allowed : 51.92 % Favored : 44.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.49 (0.48), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.37), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR B 16 HIS 0.001 0.000 HIS C 5 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 1452) covalent geometry : angle 0.75784 ( 1932) hydrogen bonds : bond 0.23874 ( 11) hydrogen bonds : angle 9.08755 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 11 time to evaluate : 0.037 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 16 average time/residue: 0.2805 time to fit residues: 4.6199 Evaluate side-chains 7 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 5 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain J residue 6 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 7 optimal weight: 0.0870 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN G 13 GLN H 13 GLN L 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.171778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.155792 restraints weight = 3101.111| |-----------------------------------------------------------------------------| r_work (start): 0.4713 rms_B_bonded: 4.61 r_work: 0.4627 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.4627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1452 Z= 0.108 Angle : 0.564 6.082 1932 Z= 0.288 Chirality : 0.055 0.131 228 Planarity : 0.002 0.006 228 Dihedral : 4.547 15.103 194 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 10.90 % Allowed : 48.08 % Favored : 41.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.21 (0.49), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.38), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR F 16 HIS 0.002 0.001 HIS B 5 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 1452) covalent geometry : angle 0.56447 ( 1932) hydrogen bonds : bond 0.02496 ( 11) hydrogen bonds : angle 6.86623 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 11 time to evaluate : 0.065 Fit side-chains REVERT: L 13 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7692 (pt0) outliers start: 17 outliers final: 1 residues processed: 25 average time/residue: 0.3291 time to fit residues: 8.4952 Evaluate side-chains 9 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain L residue 13 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 10 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 0.2980 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 13 GLN H 13 GLN L 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.168424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.152625 restraints weight = 3159.676| |-----------------------------------------------------------------------------| r_work (start): 0.4680 rms_B_bonded: 4.64 r_work (final): 0.4680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1452 Z= 0.171 Angle : 0.611 6.396 1932 Z= 0.318 Chirality : 0.056 0.139 228 Planarity : 0.002 0.006 228 Dihedral : 4.728 11.631 192 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 9.62 % Allowed : 46.79 % Favored : 43.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.03 (0.50), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.38), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR F 16 HIS 0.003 0.001 HIS B 5 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 1452) covalent geometry : angle 0.61076 ( 1932) hydrogen bonds : bond 0.02518 ( 11) hydrogen bonds : angle 6.78161 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 6 time to evaluate : 0.070 Fit side-chains REVERT: B 13 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7905 (pt0) REVERT: C 13 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.6557 (tm-30) REVERT: G 13 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.6375 (tm130) outliers start: 15 outliers final: 3 residues processed: 20 average time/residue: 0.4740 time to fit residues: 9.6913 Evaluate side-chains 12 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 6 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain I residue 15 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 9 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 0.0000 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 GLN F 13 GLN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.170077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.154050 restraints weight = 3180.793| |-----------------------------------------------------------------------------| r_work (start): 0.4800 rms_B_bonded: 4.65 r_work (final): 0.4800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1452 Z= 0.131 Angle : 0.563 5.655 1932 Z= 0.294 Chirality : 0.055 0.133 228 Planarity : 0.001 0.006 228 Dihedral : 4.597 14.894 192 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 7.69 % Allowed : 46.15 % Favored : 46.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.86 (0.51), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.39), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR F 16 HIS 0.002 0.001 HIS B 5 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 1452) covalent geometry : angle 0.56323 ( 1932) hydrogen bonds : bond 0.02037 ( 11) hydrogen bonds : angle 6.57288 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 6 time to evaluate : 0.068 Fit side-chains REVERT: B 13 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8205 (pt0) REVERT: C 13 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7197 (tm-30) REVERT: D 7 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8556 (pp) REVERT: K 13 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.6627 (tm-30) outliers start: 12 outliers final: 3 residues processed: 17 average time/residue: 0.4571 time to fit residues: 7.9831 Evaluate side-chains 13 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 6 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain K residue 13 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 2 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN G 13 GLN H 13 GLN L 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.169989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.153987 restraints weight = 3047.891| |-----------------------------------------------------------------------------| r_work (start): 0.4737 rms_B_bonded: 4.61 r_work: 0.4658 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.4658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1452 Z= 0.133 Angle : 0.552 5.274 1932 Z= 0.286 Chirality : 0.055 0.127 228 Planarity : 0.001 0.006 228 Dihedral : 4.483 11.320 192 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.57 % Favored : 95.83 % Rotamer: Outliers : 8.97 % Allowed : 46.79 % Favored : 44.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.78 (0.51), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.39), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR F 16 HIS 0.002 0.001 HIS B 5 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 1452) covalent geometry : angle 0.55221 ( 1932) hydrogen bonds : bond 0.01969 ( 11) hydrogen bonds : angle 6.24926 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 6 time to evaluate : 0.079 Fit side-chains REVERT: B 13 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.8014 (pt0) REVERT: C 13 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.6795 (tm-30) REVERT: D 7 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8056 (pp) REVERT: G 13 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.6771 (tm130) REVERT: I 15 VAL cc_start: 0.8344 (t) cc_final: 0.8122 (p) outliers start: 14 outliers final: 2 residues processed: 20 average time/residue: 0.4103 time to fit residues: 8.4316 Evaluate side-chains 12 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 6 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain G residue 13 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.171811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.156365 restraints weight = 3009.835| |-----------------------------------------------------------------------------| r_work (start): 0.4827 rms_B_bonded: 4.54 r_work (final): 0.4827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1452 Z= 0.114 Angle : 0.548 6.311 1932 Z= 0.280 Chirality : 0.055 0.128 228 Planarity : 0.001 0.006 228 Dihedral : 4.445 13.009 192 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.76 % Favored : 94.64 % Rotamer: Outliers : 6.41 % Allowed : 47.44 % Favored : 46.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.59 (0.53), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR F 16 HIS 0.002 0.001 HIS B 5 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 1452) covalent geometry : angle 0.54793 ( 1932) hydrogen bonds : bond 0.01801 ( 11) hydrogen bonds : angle 6.15167 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 10 time to evaluate : 0.070 Fit side-chains REVERT: B 13 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8275 (pt0) REVERT: C 13 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7014 (tm-30) REVERT: D 7 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8562 (pp) REVERT: I 15 VAL cc_start: 0.8668 (t) cc_final: 0.8411 (p) outliers start: 10 outliers final: 3 residues processed: 20 average time/residue: 0.3526 time to fit residues: 7.2747 Evaluate side-chains 12 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 6 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 13 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 4 optimal weight: 0.0030 chunk 6 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.182668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.165372 restraints weight = 3075.324| |-----------------------------------------------------------------------------| r_work (start): 0.4744 rms_B_bonded: 4.48 r_work (final): 0.4744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1452 Z= 0.097 Angle : 0.517 7.048 1932 Z= 0.266 Chirality : 0.054 0.127 228 Planarity : 0.001 0.006 228 Dihedral : 4.120 11.140 192 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.17 % Favored : 95.24 % Rotamer: Outliers : 4.49 % Allowed : 50.00 % Favored : 45.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.54), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.41), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR F 16 HIS 0.001 0.000 HIS B 5 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 1452) covalent geometry : angle 0.51693 ( 1932) hydrogen bonds : bond 0.01771 ( 11) hydrogen bonds : angle 5.80051 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 10 time to evaluate : 0.065 Fit side-chains REVERT: B 13 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7907 (pt0) REVERT: C 13 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.6701 (tm-30) REVERT: D 7 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8012 (pp) outliers start: 7 outliers final: 2 residues processed: 17 average time/residue: 0.3258 time to fit residues: 5.7340 Evaluate side-chains 11 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 6 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain D residue 7 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 6 optimal weight: 0.4980 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.0670 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 0.0050 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 overall best weight: 0.4732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.184687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.167345 restraints weight = 2977.439| |-----------------------------------------------------------------------------| r_work (start): 0.4770 rms_B_bonded: 4.45 r_work: 0.4665 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.4665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1452 Z= 0.089 Angle : 0.502 7.337 1932 Z= 0.257 Chirality : 0.054 0.123 228 Planarity : 0.001 0.006 228 Dihedral : 3.977 12.533 192 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.17 % Favored : 95.24 % Rotamer: Outliers : 5.13 % Allowed : 49.36 % Favored : 45.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.56), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR F 16 HIS 0.001 0.000 HIS B 5 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 1452) covalent geometry : angle 0.50185 ( 1932) hydrogen bonds : bond 0.01692 ( 11) hydrogen bonds : angle 5.69117 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 8 time to evaluate : 0.064 Fit side-chains REVERT: B 13 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7958 (pt0) REVERT: C 13 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.6530 (tm-30) REVERT: D 7 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7938 (pp) outliers start: 8 outliers final: 1 residues processed: 16 average time/residue: 0.3458 time to fit residues: 5.7284 Evaluate side-chains 11 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 7 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain D residue 7 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 5 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 0.0170 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.175871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.160324 restraints weight = 3047.623| |-----------------------------------------------------------------------------| r_work (start): 0.4757 rms_B_bonded: 4.58 r_work (final): 0.4757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1452 Z= 0.103 Angle : 0.517 7.209 1932 Z= 0.261 Chirality : 0.054 0.122 228 Planarity : 0.001 0.006 228 Dihedral : 4.023 11.622 192 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.76 % Favored : 94.64 % Rotamer: Outliers : 3.85 % Allowed : 50.64 % Favored : 45.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.56), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR F 16 HIS 0.002 0.001 HIS B 5 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 1452) covalent geometry : angle 0.51660 ( 1932) hydrogen bonds : bond 0.01590 ( 11) hydrogen bonds : angle 5.67371 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 7 time to evaluate : 0.079 Fit side-chains REVERT: B 13 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7992 (pt0) REVERT: C 13 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7823 (mm-40) REVERT: D 7 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7872 (pp) outliers start: 6 outliers final: 2 residues processed: 13 average time/residue: 0.3770 time to fit residues: 5.0880 Evaluate side-chains 11 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 6 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain F residue 3 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 5 optimal weight: 0.4980 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.184927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.167025 restraints weight = 2984.161| |-----------------------------------------------------------------------------| r_work (start): 0.4770 rms_B_bonded: 4.46 r_work: 0.4668 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.4668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1452 Z= 0.103 Angle : 0.522 7.214 1932 Z= 0.262 Chirality : 0.054 0.125 228 Planarity : 0.001 0.006 228 Dihedral : 4.019 11.850 192 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.17 % Favored : 95.24 % Rotamer: Outliers : 3.85 % Allowed : 50.64 % Favored : 45.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.56), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR F 16 HIS 0.002 0.001 HIS B 5 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 1452) covalent geometry : angle 0.52187 ( 1932) hydrogen bonds : bond 0.01598 ( 11) hydrogen bonds : angle 5.65099 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 7 time to evaluate : 0.072 Fit side-chains REVERT: B 13 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7804 (pt0) REVERT: C 13 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.6394 (tm-30) REVERT: D 7 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7807 (pp) outliers start: 6 outliers final: 2 residues processed: 13 average time/residue: 0.2666 time to fit residues: 3.6477 Evaluate side-chains 12 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 7 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain F residue 3 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 8 optimal weight: 0.0570 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 10 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 0.0060 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN F 13 GLN G 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.179458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.163212 restraints weight = 2960.061| |-----------------------------------------------------------------------------| r_work (start): 0.4824 rms_B_bonded: 4.60 r_work (final): 0.4824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1452 Z= 0.082 Angle : 0.499 7.279 1932 Z= 0.250 Chirality : 0.053 0.122 228 Planarity : 0.001 0.006 228 Dihedral : 3.767 11.690 192 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.36 % Favored : 94.05 % Rotamer: Outliers : 5.77 % Allowed : 48.72 % Favored : 45.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.58), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR I 16 HIS 0.001 0.000 HIS B 5 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 1452) covalent geometry : angle 0.49850 ( 1932) hydrogen bonds : bond 0.01686 ( 11) hydrogen bonds : angle 5.53163 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 731.79 seconds wall clock time: 14 minutes 41.76 seconds (881.76 seconds total)