Starting phenix.real_space_refine on Wed Jul 23 06:46:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v1n_42886/07_2025/8v1n_42886.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v1n_42886/07_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_42886/07_2025/8v1n_42886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v1n_42886/07_2025/8v1n_42886.map" model { file = "/net/cci-nas-00/data/ceres_data/8v1n_42886/07_2025/8v1n_42886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v1n_42886/07_2025/8v1n_42886.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 1.14, per 1000 atoms: 0.79 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: 0.92 Conformation dependent library (CDL) restraints added in 151.6 milliseconds 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: 0.21 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: 0.36 Time building geometry restraints manager: 0.99 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: 2.240 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.970 Find NCS groups from input model: 0.070 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:10.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.370 ------------------------------------------------------------------------------- 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 : 14.70 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.001 0.000 HIS C 5 TYR 0.010 0.001 TYR B 16 Details of bonding type rmsd hydrogen bonds : bond 0.23874 ( 11) hydrogen bonds : angle 9.08755 ( 33) covalent geometry : bond 0.00355 ( 1452) covalent geometry : angle 0.75784 ( 1932) *********************** 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 : 0.179 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 16 average time/residue: 0.8321 time to fit residues: 13.7949 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 : 0.191 ------------------------------------------------------------------------------- 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 10 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 L 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.164661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.149418 restraints weight = 3185.762| |-----------------------------------------------------------------------------| r_work (start): 0.4636 rms_B_bonded: 4.50 r_work: 0.4521 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 1452 Z= 0.226 Angle : 0.671 6.596 1932 Z= 0.345 Chirality : 0.057 0.136 228 Planarity : 0.002 0.006 228 Dihedral : 5.668 25.625 194 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 12.18 % Allowed : 42.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.49), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.37), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 5 TYR 0.014 0.002 TYR F 16 Details of bonding type rmsd hydrogen bonds : bond 0.02681 ( 11) hydrogen bonds : angle 7.04374 ( 33) covalent geometry : bond 0.00578 ( 1452) covalent geometry : angle 0.67077 ( 1932) *********************** 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 25 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 6 time to evaluate : 0.177 Fit side-chains REVERT: C 13 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7631 (mm-40) REVERT: L 13 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7295 (pt0) outliers start: 19 outliers final: 4 residues processed: 23 average time/residue: 0.7804 time to fit residues: 18.4861 Evaluate side-chains 10 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 4 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain J residue 6 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 4 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 F 13 GLN G 13 GLN H 13 GLN L 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.167063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.151429 restraints weight = 3153.813| |-----------------------------------------------------------------------------| r_work (start): 0.4665 rms_B_bonded: 4.61 r_work (final): 0.4665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1452 Z= 0.156 Angle : 0.599 7.689 1932 Z= 0.310 Chirality : 0.056 0.132 228 Planarity : 0.002 0.006 228 Dihedral : 5.136 19.645 194 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 11.54 % Allowed : 44.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.48), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.37), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 5 TYR 0.009 0.001 TYR F 16 Details of bonding type rmsd hydrogen bonds : bond 0.02622 ( 11) hydrogen bonds : angle 6.65986 ( 33) covalent geometry : bond 0.00395 ( 1452) covalent geometry : angle 0.59923 ( 1932) *********************** 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 24 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 6 time to evaluate : 0.185 Fit side-chains REVERT: L 13 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7465 (pt0) outliers start: 18 outliers final: 5 residues processed: 23 average time/residue: 0.8533 time to fit residues: 20.1734 Evaluate side-chains 11 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 5 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain L residue 13 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.0010 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4840 r_free = 0.4840 target = 0.171278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.155427 restraints weight = 3031.395| |-----------------------------------------------------------------------------| r_work (start): 0.4736 rms_B_bonded: 4.55 r_work: 0.4660 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.4660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1452 Z= 0.104 Angle : 0.532 6.545 1932 Z= 0.280 Chirality : 0.055 0.134 228 Planarity : 0.001 0.007 228 Dihedral : 4.663 15.558 194 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.76 % Favored : 94.64 % Rotamer: Outliers : 12.18 % Allowed : 43.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.49), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.37), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 5 TYR 0.006 0.001 TYR F 16 Details of bonding type rmsd hydrogen bonds : bond 0.02285 ( 11) hydrogen bonds : angle 6.46307 ( 33) covalent geometry : bond 0.00252 ( 1452) covalent geometry : angle 0.53180 ( 1932) *********************** 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 27 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 8 time to evaluate : 0.189 Fit side-chains REVERT: C 1 ASP cc_start: 0.5538 (OUTLIER) cc_final: 0.5262 (t0) REVERT: C 13 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.6765 (tm-30) REVERT: D 7 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8032 (pp) REVERT: K 13 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.6282 (tm-30) outliers start: 19 outliers final: 3 residues processed: 26 average time/residue: 0.9907 time to fit residues: 26.3776 Evaluate side-chains 12 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 5 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain C residue 1 ASP 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 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 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 0.0970 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 13 GLN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4854 r_free = 0.4854 target = 0.172617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.157668 restraints weight = 2954.435| |-----------------------------------------------------------------------------| r_work (start): 0.4834 rms_B_bonded: 4.44 r_work: 0.4705 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.4705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1452 Z= 0.102 Angle : 0.530 5.843 1932 Z= 0.280 Chirality : 0.054 0.131 228 Planarity : 0.001 0.006 228 Dihedral : 4.520 14.892 193 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.76 % Favored : 94.64 % Rotamer: Outliers : 7.69 % Allowed : 46.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.52), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 5 TYR 0.006 0.001 TYR F 16 Details of bonding type rmsd hydrogen bonds : bond 0.02065 ( 11) hydrogen bonds : angle 6.42433 ( 33) covalent geometry : bond 0.00244 ( 1452) covalent geometry : angle 0.52993 ( 1932) *********************** 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 22 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 10 time to evaluate : 0.213 Fit side-chains REVERT: B 13 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7448 (pt0) REVERT: C 13 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8075 (mm-40) REVERT: D 7 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8545 (pp) outliers start: 12 outliers final: 1 residues processed: 22 average time/residue: 0.6654 time to fit residues: 15.2253 Evaluate side-chains 12 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 8 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.171010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.155934 restraints weight = 3008.248| |-----------------------------------------------------------------------------| r_work (start): 0.4716 rms_B_bonded: 4.49 r_work (final): 0.4716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1452 Z= 0.135 Angle : 0.555 5.662 1932 Z= 0.287 Chirality : 0.055 0.134 228 Planarity : 0.001 0.007 228 Dihedral : 4.487 11.525 192 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.14 % Favored : 92.26 % Rotamer: Outliers : 8.33 % Allowed : 46.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.53), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 5 TYR 0.009 0.001 TYR F 16 Details of bonding type rmsd hydrogen bonds : bond 0.02040 ( 11) hydrogen bonds : angle 6.06987 ( 33) covalent geometry : bond 0.00349 ( 1452) covalent geometry : angle 0.55512 ( 1932) *********************** 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: 13 poor density : 7 time to evaluate : 0.197 Fit side-chains REVERT: B 13 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.7199 (pt0) REVERT: C 13 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.6438 (tm-30) REVERT: D 7 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7914 (pp) outliers start: 13 outliers final: 3 residues processed: 20 average time/residue: 0.9501 time to fit residues: 19.5257 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 : 0.186 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 2 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.4860 r_free = 0.4860 target = 0.173153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.157950 restraints weight = 3054.218| |-----------------------------------------------------------------------------| r_work (start): 0.4844 rms_B_bonded: 4.58 r_work (final): 0.4844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2486 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= 0.100 Angle : 0.530 6.960 1932 Z= 0.271 Chirality : 0.054 0.127 228 Planarity : 0.001 0.006 228 Dihedral : 4.246 12.096 192 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.36 % Favored : 94.05 % Rotamer: Outliers : 5.77 % Allowed : 50.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.54), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.41), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 5 TYR 0.007 0.001 TYR F 16 Details of bonding type rmsd hydrogen bonds : bond 0.01858 ( 11) hydrogen bonds : angle 6.14525 ( 33) covalent geometry : bond 0.00247 ( 1452) covalent geometry : angle 0.52994 ( 1932) *********************** 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: 9 poor density : 8 time to evaluate : 0.190 Fit side-chains REVERT: B 4 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7143 (tmtt) REVERT: C 13 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7986 (mm-40) REVERT: D 7 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8542 (pp) outliers start: 9 outliers final: 2 residues processed: 17 average time/residue: 0.8422 time to fit residues: 14.8042 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 : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 6 VAL 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 11 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.4782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.169520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.154012 restraints weight = 3060.646| |-----------------------------------------------------------------------------| r_work (start): 0.4696 rms_B_bonded: 4.57 r_work (final): 0.4696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6068 moved from start: 0.2557 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= 0.158 Angle : 0.579 6.575 1932 Z= 0.295 Chirality : 0.054 0.127 228 Planarity : 0.002 0.006 228 Dihedral : 4.594 11.808 192 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.36 % Favored : 94.05 % Rotamer: Outliers : 6.41 % Allowed : 49.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.53), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 5 TYR 0.011 0.001 TYR F 16 Details of bonding type rmsd hydrogen bonds : bond 0.02095 ( 11) hydrogen bonds : angle 6.03817 ( 33) covalent geometry : bond 0.00405 ( 1452) covalent geometry : angle 0.57938 ( 1932) *********************** 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 17 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 7 time to evaluate : 0.189 Fit side-chains REVERT: B 4 LYS cc_start: 0.6738 (OUTLIER) cc_final: 0.6142 (tmtt) REVERT: C 13 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.5958 (tm-30) REVERT: D 7 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7602 (pp) outliers start: 10 outliers final: 2 residues processed: 17 average time/residue: 0.9460 time to fit residues: 16.5903 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 : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 6 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.174820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.159137 restraints weight = 3053.667| |-----------------------------------------------------------------------------| r_work (start): 0.4772 rms_B_bonded: 4.76 r_work (final): 0.4772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1452 Z= 0.161 Angle : 0.584 7.241 1932 Z= 0.296 Chirality : 0.054 0.131 228 Planarity : 0.002 0.006 228 Dihedral : 4.636 11.918 192 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.76 % Favored : 94.64 % Rotamer: Outliers : 7.05 % Allowed : 47.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.52), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 5 TYR 0.011 0.001 TYR F 16 Details of bonding type rmsd hydrogen bonds : bond 0.02057 ( 11) hydrogen bonds : angle 6.06468 ( 33) covalent geometry : bond 0.00414 ( 1452) covalent geometry : angle 0.58363 ( 1932) *********************** 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 18 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 7 time to evaluate : 0.172 Fit side-chains REVERT: B 4 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7308 (tmtt) REVERT: C 13 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.6621 (tm-30) REVERT: D 7 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8702 (pp) outliers start: 11 outliers final: 3 residues processed: 18 average time/residue: 0.9912 time to fit residues: 18.3195 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 : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 8 optimal weight: 0.2980 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 overall best weight: 0.6560 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.178325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.163310 restraints weight = 2922.021| |-----------------------------------------------------------------------------| r_work (start): 0.4854 rms_B_bonded: 4.44 r_work: 0.4725 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.4725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1452 Z= 0.108 Angle : 0.545 7.666 1932 Z= 0.273 Chirality : 0.054 0.125 228 Planarity : 0.001 0.006 228 Dihedral : 4.299 12.081 192 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.17 % Favored : 95.24 % Rotamer: Outliers : 5.77 % Allowed : 49.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.54), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.41), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 5 TYR 0.006 0.001 TYR F 16 Details of bonding type rmsd hydrogen bonds : bond 0.01886 ( 11) hydrogen bonds : angle 6.35976 ( 33) covalent geometry : bond 0.00261 ( 1452) covalent geometry : angle 0.54489 ( 1932) ********************** 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 18 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 9 time to evaluate : 0.181 Fit side-chains REVERT: B 4 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7360 (tmtt) REVERT: C 13 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: D 7 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8797 (pp) outliers start: 9 outliers final: 2 residues processed: 18 average time/residue: 0.7856 time to fit residues: 14.6735 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 : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 6 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 0.0970 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 0 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.179000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.163983 restraints weight = 2941.639| |-----------------------------------------------------------------------------| r_work (start): 0.4759 rms_B_bonded: 4.45 r_work: 0.4657 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.4657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5888 moved from start: 0.2923 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= 0.105 Angle : 0.540 7.422 1932 Z= 0.268 Chirality : 0.054 0.126 228 Planarity : 0.001 0.006 228 Dihedral : 4.178 12.354 192 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.36 % Favored : 94.05 % Rotamer: Outliers : 4.49 % Allowed : 51.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.55), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 5 TYR 0.006 0.001 TYR F 16 Details of bonding type rmsd hydrogen bonds : bond 0.01750 ( 11) hydrogen bonds : angle 6.13235 ( 33) covalent geometry : bond 0.00259 ( 1452) covalent geometry : angle 0.54009 ( 1932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1405.56 seconds wall clock time: 24 minutes 47.03 seconds (1487.03 seconds total)