Starting phenix.real_space_refine on Mon Jan 13 12:52:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v1n_42886/01_2025/8v1n_42886.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v1n_42886/01_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_42886/01_2025/8v1n_42886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v1n_42886/01_2025/8v1n_42886.map" model { file = "/net/cci-nas-00/data/ceres_data/8v1n_42886/01_2025/8v1n_42886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v1n_42886/01_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-5571/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: 1.24, per 1000 atoms: 0.86 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: 0.40 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 0.26 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: 0.32 Time building geometry restraints manager: 0.48 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: 2.930 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.230 Find NCS groups from input model: 0.120 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.810 ------------------------------------------------------------------------------- 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= 0.257 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 *********************** 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 : 0.187 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 16 average time/residue: 0.7648 time to fit residues: 12.7075 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 : 0.188 ------------------------------------------------------------------------------- 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: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.164429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.149255 restraints weight = 3178.904| |-----------------------------------------------------------------------------| r_work (start): 0.4630 rms_B_bonded: 4.51 r_work: 0.4518 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.4518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6123 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 1452 Z= 0.397 Angle : 0.675 6.748 1932 Z= 0.346 Chirality : 0.057 0.134 228 Planarity : 0.002 0.006 228 Dihedral : 5.719 25.508 194 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 13.46 % Allowed : 41.03 % 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: -3.44 (0.49), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.38), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 5 TYR 0.015 0.002 TYR F 16 *********************** 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 27 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 6 time to evaluate : 0.191 Fit side-chains REVERT: C 13 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7542 (mm-40) outliers start: 21 outliers final: 5 residues processed: 25 average time/residue: 0.8349 time to fit residues: 21.4618 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 : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 ILE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 4 optimal weight: 0.0020 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 overall best weight: 1.9394 ------------------------------------------------------------------------------- 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 = 0.4788 r_free = 0.4788 target = 0.165879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.150389 restraints weight = 3178.616| |-----------------------------------------------------------------------------| r_work (start): 0.4747 rms_B_bonded: 4.58 r_work (final): 0.4747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 1452 Z= 0.349 Angle : 0.627 8.026 1932 Z= 0.324 Chirality : 0.057 0.135 228 Planarity : 0.002 0.006 228 Dihedral : 5.317 20.891 194 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 12.82 % Allowed : 42.95 % 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 (0.49), 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 *********************** 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: 20 poor density : 4 time to evaluate : 0.196 Fit side-chains REVERT: A 7 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6943 (pt) REVERT: C 13 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8050 (mm-40) outliers start: 20 outliers final: 5 residues processed: 23 average time/residue: 0.7714 time to fit residues: 18.3083 Evaluate side-chains 11 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 4 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU 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 E residue 15 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain J residue 6 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 11 optimal weight: 6.9990 chunk 9 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 8 optimal weight: 0.0000 chunk 4 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 overall best weight: 0.4582 ------------------------------------------------------------------------------- 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 = 0.4882 r_free = 0.4882 target = 0.175833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.160073 restraints weight = 2975.186| |-----------------------------------------------------------------------------| r_work (start): 0.4848 rms_B_bonded: 4.54 r_work: 0.4727 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.4727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1452 Z= 0.142 Angle : 0.504 6.091 1932 Z= 0.266 Chirality : 0.055 0.132 228 Planarity : 0.001 0.006 228 Dihedral : 4.368 12.206 194 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 7.69 % Allowed : 47.44 % 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: -2.99 (0.50), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.38), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 5 TYR 0.004 0.001 TYR J 16 *********************** 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 23 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 11 time to evaluate : 0.187 Fit side-chains REVERT: C 13 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: D 7 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8552 (pp) REVERT: L 14 ILE cc_start: 0.8841 (mt) cc_final: 0.8620 (mp) outliers start: 12 outliers final: 1 residues processed: 21 average time/residue: 0.7845 time to fit residues: 17.0176 Evaluate side-chains 10 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 7 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.4857 r_free = 0.4857 target = 0.173053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.157500 restraints weight = 2965.014| |-----------------------------------------------------------------------------| r_work (start): 0.4824 rms_B_bonded: 4.53 r_work (final): 0.4824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2322 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= 0.203 Angle : 0.542 5.916 1932 Z= 0.282 Chirality : 0.055 0.135 228 Planarity : 0.001 0.006 228 Dihedral : 4.361 11.830 192 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.36 % Favored : 94.05 % Rotamer: Outliers : 7.05 % Allowed : 48.72 % 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: -2.79 (0.52), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 5 TYR 0.007 0.001 TYR F 16 *********************** 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 19 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 8 time to evaluate : 0.193 Fit side-chains REVERT: C 13 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.6918 (tm-30) REVERT: D 7 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8582 (pp) REVERT: I 15 VAL cc_start: 0.8842 (t) cc_final: 0.8607 (p) outliers start: 11 outliers final: 4 residues processed: 19 average time/residue: 0.9877 time to fit residues: 19.2775 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 : 0.173 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain H 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: 4.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.172981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.157791 restraints weight = 3003.755| |-----------------------------------------------------------------------------| r_work (start): 0.4749 rms_B_bonded: 4.49 r_work: 0.4663 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.4663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.2401 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= 0.214 Angle : 0.549 5.424 1932 Z= 0.282 Chirality : 0.055 0.130 228 Planarity : 0.001 0.006 228 Dihedral : 4.346 12.672 192 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.36 % Favored : 94.05 % Rotamer: Outliers : 6.41 % Allowed : 50.00 % 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: -2.57 (0.53), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 5 TYR 0.007 0.001 TYR F 16 *********************** 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 : 0.191 Fit side-chains REVERT: C 13 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.6882 (tm-30) REVERT: D 7 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8083 (pp) REVERT: I 15 VAL cc_start: 0.8576 (t) cc_final: 0.8346 (p) REVERT: K 13 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.6243 (tm-30) outliers start: 10 outliers final: 3 residues processed: 20 average time/residue: 0.5899 time to fit residues: 12.3253 Evaluate side-chains 14 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 8 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 K 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: 7.9990 chunk 5 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- 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 = 0.4806 r_free = 0.4806 target = 0.170705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.155241 restraints weight = 3018.513| |-----------------------------------------------------------------------------| r_work (start): 0.4745 rms_B_bonded: 4.65 r_work (final): 0.4745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 1452 Z= 0.356 Angle : 0.634 6.170 1932 Z= 0.321 Chirality : 0.056 0.130 228 Planarity : 0.002 0.006 228 Dihedral : 4.874 12.343 192 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.55 % Favored : 92.86 % Rotamer: Outliers : 7.05 % Allowed : 48.08 % 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: -2.60 (0.52), 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 HIS 0.004 0.001 HIS B 5 TYR 0.012 0.002 TYR F 16 *********************** 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 18 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 7 time to evaluate : 0.192 Fit side-chains REVERT: B 4 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7196 (tmtt) REVERT: C 13 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.6656 (tm-30) REVERT: D 7 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8572 (pp) REVERT: I 15 VAL cc_start: 0.8777 (t) cc_final: 0.8502 (p) REVERT: K 13 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.6628 (tm-30) outliers start: 11 outliers final: 2 residues processed: 18 average time/residue: 0.9490 time to fit residues: 17.6295 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 : 0.215 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain K residue 13 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 overall best weight: 1.3080 ------------------------------------------------------------------------------- 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 = 0.175865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.161125 restraints weight = 2882.542| |-----------------------------------------------------------------------------| r_work (start): 0.4750 rms_B_bonded: 4.32 r_work: 0.4645 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.4645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1452 Z= 0.257 Angle : 0.601 7.144 1932 Z= 0.300 Chirality : 0.055 0.129 228 Planarity : 0.001 0.006 228 Dihedral : 4.629 11.875 192 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 10.69 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: -2.51 (0.53), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 5 TYR 0.008 0.001 TYR F 16 *********************** 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 21 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 9 time to evaluate : 0.196 Fit side-chains REVERT: B 4 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7402 (tmtt) REVERT: C 13 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.6813 (tm-30) REVERT: D 7 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8707 (pp) REVERT: K 13 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.6551 (tm-30) outliers start: 12 outliers final: 2 residues processed: 21 average time/residue: 0.7025 time to fit residues: 15.3168 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 : 0.192 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain K residue 13 GLN 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: 4.9990 chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4871 r_free = 0.4871 target = 0.175093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.160138 restraints weight = 3002.717| |-----------------------------------------------------------------------------| r_work (start): 0.4740 rms_B_bonded: 4.43 r_work: 0.4639 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.4639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1452 Z= 0.268 Angle : 0.644 9.001 1932 Z= 0.313 Chirality : 0.056 0.138 228 Planarity : 0.001 0.006 228 Dihedral : 4.719 12.021 192 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.36 % Favored : 94.05 % Rotamer: Outliers : 5.77 % Allowed : 46.15 % Favored : 48.08 % 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: -2.48 (0.54), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.41), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 5 TYR 0.008 0.001 TYR F 16 *********************** 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 15 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 6 time to evaluate : 0.203 Fit side-chains REVERT: B 4 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7369 (tmtt) REVERT: C 13 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.6783 (tm-30) REVERT: D 7 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8684 (pp) REVERT: K 13 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.6486 (tm-30) outliers start: 9 outliers final: 2 residues processed: 15 average time/residue: 0.8703 time to fit residues: 13.5224 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 : 0.195 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain K residue 13 GLN 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 9 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 0.0170 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 0.0770 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.4916 r_free = 0.4916 target = 0.180285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.165038 restraints weight = 2874.330| |-----------------------------------------------------------------------------| r_work (start): 0.4808 rms_B_bonded: 4.45 r_work: 0.4706 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.4706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1452 Z= 0.160 Angle : 0.591 8.025 1932 Z= 0.283 Chirality : 0.055 0.129 228 Planarity : 0.001 0.006 228 Dihedral : 4.361 14.579 192 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 1.19 % Allowed : 4.76 % Favored : 94.05 % Rotamer: Outliers : 3.85 % Allowed : 48.08 % Favored : 48.08 % 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: -2.22 (0.56), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 5 TYR 0.004 0.001 TYR F 16 ********************** 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 17 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 11 time to evaluate : 0.180 Fit side-chains REVERT: B 4 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7202 (tmtt) REVERT: C 13 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.6861 (tm-30) REVERT: D 7 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8745 (pp) outliers start: 6 outliers final: 1 residues processed: 17 average time/residue: 0.7138 time to fit residues: 12.6041 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 : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain E residue 2 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.178852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.164054 restraints weight = 2903.737| |-----------------------------------------------------------------------------| r_work (start): 0.4804 rms_B_bonded: 4.40 r_work: 0.4698 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.4698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1452 Z= 0.200 Angle : 0.598 7.915 1932 Z= 0.287 Chirality : 0.055 0.128 228 Planarity : 0.001 0.006 228 Dihedral : 4.428 14.343 192 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 1.19 % Allowed : 5.36 % Favored : 93.45 % Rotamer: Outliers : 4.49 % Allowed : 49.36 % 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 (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: -2.20 (0.56), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 5 TYR 0.006 0.001 TYR F 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1292.32 seconds wall clock time: 23 minutes 43.27 seconds (1423.27 seconds total)