Starting phenix.real_space_refine on Fri May 9 14:54:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xwd_38733/05_2025/8xwd_38733.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xwd_38733/05_2025/8xwd_38733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xwd_38733/05_2025/8xwd_38733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xwd_38733/05_2025/8xwd_38733.map" model { file = "/net/cci-nas-00/data/ceres_data/8xwd_38733/05_2025/8xwd_38733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xwd_38733/05_2025/8xwd_38733.cif" } resolution = 3.1 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= 0.002 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 1686 2.51 5 N 426 2.21 5 O 558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2670 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 412 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "D" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 412 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "E" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 412 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "A" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 412 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "F" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 412 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "B" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 412 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KDH': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KDH': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KDH': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KDH': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KDH': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KDH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.78, per 1000 atoms: 1.04 Number of scatterers: 2670 At special positions: 0 Unit cell: (97.11, 98.77, 31.54, 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 558 8.00 N 426 7.00 C 1686 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: 0.77 Conformation dependent library (CDL) restraints added in 342.5 milliseconds 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 612 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 46 through 56 removed outlier: 6.858A pdb=" N GLY C 47 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL E 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA C 53 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR E 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL C 55 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA E 56 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLY C 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N HIS F 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N VAL C 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N VAL F 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY C 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N THR F 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ALA F 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL C 55 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 69 through 71 removed outlier: 6.532A pdb=" N VAL C 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 75 through 77 removed outlier: 8.643A pdb=" N THR C 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL F 77 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 80 through 82 removed outlier: 6.499A pdb=" N LYS C 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 46 through 56 removed outlier: 6.831A pdb=" N VAL D 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N HIS D 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY A 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLU D 46 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N VAL B 49 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL D 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N GLY B 51 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N HIS D 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N ALA B 53 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL D 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N VAL B 55 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N THR D 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.538A pdb=" N VAL D 70 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 75 through 77 removed outlier: 8.656A pdb=" N THR D 75 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 77 " --> pdb=" O ALA D 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 80 through 82 removed outlier: 6.516A pdb=" N LYS D 80 " --> pdb=" O THR A 81 " (cutoff:3.500A) 20 hydrogen bonds defined for protein. 60 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: 0.53 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.27: 432 1.27 - 1.34: 384 1.34 - 1.41: 270 1.41 - 1.48: 444 1.48 - 1.55: 1170 Bond restraints: 2700 Sorted by residual: bond pdb=" CB VAL D 40 " pdb=" CG1 VAL D 40 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.91e+00 bond pdb=" CB VAL A 40 " pdb=" CG1 VAL A 40 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.91e+00 bond pdb=" CB VAL F 40 " pdb=" CG1 VAL F 40 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.90e+00 bond pdb=" CB VAL E 40 " pdb=" CG1 VAL E 40 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.80e+00 bond pdb=" CB VAL B 40 " pdb=" CG1 VAL B 40 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.80e+00 ... (remaining 2695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 2879 0.94 - 1.89: 524 1.89 - 2.83: 179 2.83 - 3.77: 71 3.77 - 4.71: 37 Bond angle restraints: 3690 Sorted by residual: angle pdb=" N GLY D 73 " pdb=" CA GLY D 73 " pdb=" C GLY D 73 " ideal model delta sigma weight residual 114.10 118.21 -4.11 1.51e+00 4.39e-01 7.42e+00 angle pdb=" N GLY C 73 " pdb=" CA GLY C 73 " pdb=" C GLY C 73 " ideal model delta sigma weight residual 114.10 118.21 -4.11 1.51e+00 4.39e-01 7.40e+00 angle pdb=" N GLY B 73 " pdb=" CA GLY B 73 " pdb=" C GLY B 73 " ideal model delta sigma weight residual 114.10 118.20 -4.10 1.51e+00 4.39e-01 7.39e+00 angle pdb=" N GLY E 73 " pdb=" CA GLY E 73 " pdb=" C GLY E 73 " ideal model delta sigma weight residual 114.10 118.20 -4.10 1.51e+00 4.39e-01 7.38e+00 angle pdb=" N GLY A 73 " pdb=" CA GLY A 73 " pdb=" C GLY A 73 " ideal model delta sigma weight residual 114.10 118.18 -4.08 1.51e+00 4.39e-01 7.31e+00 ... (remaining 3685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.89: 1476 25.89 - 51.77: 60 51.77 - 77.66: 6 77.66 - 103.54: 0 103.54 - 129.43: 6 Dihedral angle restraints: 1548 sinusoidal: 576 harmonic: 972 Sorted by residual: dihedral pdb=" C33 KDH D 501 " pdb=" C36 KDH D 501 " pdb=" O35 KDH D 501 " pdb=" C38 KDH D 501 " ideal model delta sinusoidal sigma weight residual 166.64 -63.93 -129.43 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C33 KDH A 501 " pdb=" C36 KDH A 501 " pdb=" O35 KDH A 501 " pdb=" C38 KDH A 501 " ideal model delta sinusoidal sigma weight residual 166.64 -64.00 -129.36 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C33 KDH B 501 " pdb=" C36 KDH B 501 " pdb=" O35 KDH B 501 " pdb=" C38 KDH B 501 " ideal model delta sinusoidal sigma weight residual 166.64 -64.02 -129.34 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 1545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 203 0.037 - 0.074: 139 0.074 - 0.111: 74 0.111 - 0.148: 34 0.148 - 0.185: 12 Chirality restraints: 462 Sorted by residual: chirality pdb=" CB VAL D 40 " pdb=" CA VAL D 40 " pdb=" CG1 VAL D 40 " pdb=" CG2 VAL D 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CB VAL F 40 " pdb=" CA VAL F 40 " pdb=" CG1 VAL F 40 " pdb=" CG2 VAL F 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CB VAL C 40 " pdb=" CA VAL C 40 " pdb=" CG1 VAL C 40 " pdb=" CG2 VAL C 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 459 not shown) Planarity restraints: 438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 50 " 0.012 2.00e-02 2.50e+03 1.05e-02 1.64e+00 pdb=" CG HIS B 50 " -0.022 2.00e-02 2.50e+03 pdb=" ND1 HIS B 50 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS B 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS B 50 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS B 50 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 50 " 0.012 2.00e-02 2.50e+03 1.03e-02 1.60e+00 pdb=" CG HIS A 50 " -0.021 2.00e-02 2.50e+03 pdb=" ND1 HIS A 50 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS A 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS A 50 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS A 50 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 50 " -0.012 2.00e-02 2.50e+03 1.03e-02 1.58e+00 pdb=" CG HIS F 50 " 0.021 2.00e-02 2.50e+03 pdb=" ND1 HIS F 50 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS F 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS F 50 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS F 50 " -0.005 2.00e-02 2.50e+03 ... (remaining 435 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 493 2.76 - 3.29: 2485 3.29 - 3.83: 3858 3.83 - 4.36: 4344 4.36 - 4.90: 9687 Nonbonded interactions: 20867 Sorted by model distance: nonbonded pdb=" NE2 GLN C 79 " pdb=" O GLY E 86 " model vdw 2.222 3.120 nonbonded pdb=" O GLY D 86 " pdb=" NE2 GLN B 79 " model vdw 2.228 3.120 nonbonded pdb=" O GLY C 86 " pdb=" NE2 GLN F 79 " model vdw 2.229 3.120 nonbonded pdb=" NE2 GLN D 79 " pdb=" O GLY A 86 " model vdw 2.237 3.120 nonbonded pdb=" C4 KDH C 501 " pdb=" O37 KDH F 501 " model vdw 2.425 3.340 ... (remaining 20862 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 1.990 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.120 Find NCS groups from input model: 0.060 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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 : 0.010 0.056 2700 Z= 0.432 Angle : 1.016 4.713 3690 Z= 0.530 Chirality : 0.066 0.185 462 Planarity : 0.003 0.010 438 Dihedral : 17.290 129.429 936 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.41 % Favored : 77.59 % Rotamer: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % 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: -4.55 (0.39), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.005 HIS B 50 PHE 0.008 0.003 PHE E 94 TYR 0.017 0.004 TYR A 39 Details of bonding type rmsd hydrogen bonds : bond 0.18335 ( 20) hydrogen bonds : angle 7.69179 ( 60) covalent geometry : bond 0.00977 ( 2700) covalent geometry : angle 1.01607 ( 3690) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.282 Fit side-chains REVERT: C 43 LYS cc_start: 0.7848 (ptpp) cc_final: 0.7591 (ptpp) REVERT: E 43 LYS cc_start: 0.8258 (ptpp) cc_final: 0.7936 (ptpp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.2147 time to fit residues: 7.5086 Evaluate side-chains 29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.126434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.084479 restraints weight = 3308.526| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.34 r_work: 0.3230 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2700 Z= 0.115 Angle : 0.667 4.884 3690 Z= 0.348 Chirality : 0.059 0.157 462 Planarity : 0.002 0.006 438 Dihedral : 15.724 87.157 468 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer: Outliers : 3.17 % Allowed : 7.14 % Favored : 89.68 % 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: -3.35 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.009 0.002 PHE D 94 TYR 0.008 0.002 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.02322 ( 20) hydrogen bonds : angle 5.60536 ( 60) covalent geometry : bond 0.00245 ( 2700) covalent geometry : angle 0.66664 ( 3690) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.283 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 28 average time/residue: 0.1964 time to fit residues: 6.5704 Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.130314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.086575 restraints weight = 3184.533| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.42 r_work: 0.3137 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2700 Z= 0.236 Angle : 0.705 3.997 3690 Z= 0.384 Chirality : 0.058 0.143 462 Planarity : 0.002 0.009 438 Dihedral : 15.334 87.804 468 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.54 % Favored : 80.46 % Rotamer: Outliers : 6.35 % Allowed : 4.76 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.16 (0.45), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS C 50 PHE 0.009 0.003 PHE D 94 TYR 0.006 0.001 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.02652 ( 20) hydrogen bonds : angle 5.55083 ( 60) covalent geometry : bond 0.00547 ( 2700) covalent geometry : angle 0.70489 ( 3690) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 28 time to evaluate : 0.273 Fit side-chains REVERT: C 43 LYS cc_start: 0.7266 (ptpp) cc_final: 0.6951 (ptpp) REVERT: E 43 LYS cc_start: 0.7889 (ptpp) cc_final: 0.7601 (ptpp) REVERT: F 43 LYS cc_start: 0.7654 (ptpp) cc_final: 0.7392 (ptpp) outliers start: 16 outliers final: 16 residues processed: 40 average time/residue: 0.1748 time to fit residues: 8.3165 Evaluate side-chains 42 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 26 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 10.0000 chunk 25 optimal weight: 0.0170 chunk 29 optimal weight: 0.0370 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.127759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.087031 restraints weight = 3371.805| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.33 r_work: 0.3288 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2700 Z= 0.090 Angle : 0.537 3.841 3690 Z= 0.288 Chirality : 0.054 0.134 462 Planarity : 0.001 0.005 438 Dihedral : 13.745 83.979 468 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.08 % Favored : 85.92 % Rotamer: Outliers : 2.78 % Allowed : 7.54 % Favored : 89.68 % 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 (0.47), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS E 50 PHE 0.007 0.002 PHE C 94 TYR 0.005 0.001 TYR A 39 Details of bonding type rmsd hydrogen bonds : bond 0.01944 ( 20) hydrogen bonds : angle 5.48603 ( 60) covalent geometry : bond 0.00190 ( 2700) covalent geometry : angle 0.53664 ( 3690) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.288 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 25 average time/residue: 0.1876 time to fit residues: 5.6567 Evaluate side-chains 25 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 26 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.122333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.081134 restraints weight = 3436.798| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.38 r_work: 0.3296 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2700 Z= 0.198 Angle : 0.611 3.999 3690 Z= 0.338 Chirality : 0.055 0.135 462 Planarity : 0.002 0.008 438 Dihedral : 13.859 81.232 468 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.38 % Favored : 83.62 % Rotamer: Outliers : 5.95 % Allowed : 6.35 % Favored : 87.70 % 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 (0.46), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS D 50 PHE 0.010 0.002 PHE D 94 TYR 0.005 0.001 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.02269 ( 20) hydrogen bonds : angle 5.49785 ( 60) covalent geometry : bond 0.00459 ( 2700) covalent geometry : angle 0.61061 ( 3690) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 22 time to evaluate : 0.258 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 34 average time/residue: 0.1548 time to fit residues: 6.4213 Evaluate side-chains 37 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 22 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 12 optimal weight: 0.4980 chunk 18 optimal weight: 0.3980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.131164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.085564 restraints weight = 3089.750| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.55 r_work: 0.3207 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2700 Z= 0.172 Angle : 0.587 3.970 3690 Z= 0.324 Chirality : 0.054 0.133 462 Planarity : 0.002 0.008 438 Dihedral : 13.476 78.152 468 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.08 % Favored : 85.92 % Rotamer: Outliers : 5.16 % Allowed : 7.94 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.34 (0.47), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS D 50 PHE 0.009 0.002 PHE D 94 TYR 0.004 0.001 TYR A 39 Details of bonding type rmsd hydrogen bonds : bond 0.02126 ( 20) hydrogen bonds : angle 5.46586 ( 60) covalent geometry : bond 0.00392 ( 2700) covalent geometry : angle 0.58739 ( 3690) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 22 time to evaluate : 0.283 Fit side-chains outliers start: 13 outliers final: 13 residues processed: 31 average time/residue: 0.1680 time to fit residues: 6.3118 Evaluate side-chains 35 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 22 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 0.4980 chunk 27 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.125359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.085551 restraints weight = 3545.336| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.43 r_work: 0.3429 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2700 Z= 0.101 Angle : 0.504 4.129 3690 Z= 0.278 Chirality : 0.052 0.131 462 Planarity : 0.001 0.007 438 Dihedral : 12.721 76.882 468 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.22 % Favored : 86.78 % Rotamer: Outliers : 5.56 % Allowed : 7.54 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.11 (0.48), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 50 PHE 0.007 0.001 PHE D 94 TYR 0.004 0.001 TYR A 39 Details of bonding type rmsd hydrogen bonds : bond 0.01816 ( 20) hydrogen bonds : angle 5.43230 ( 60) covalent geometry : bond 0.00221 ( 2700) covalent geometry : angle 0.50364 ( 3690) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 19 time to evaluate : 0.243 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 31 average time/residue: 0.1525 time to fit residues: 5.7735 Evaluate side-chains 32 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 19 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.128146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.083098 restraints weight = 3117.738| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.56 r_work: 0.3163 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2700 Z= 0.224 Angle : 0.611 4.303 3690 Z= 0.340 Chirality : 0.054 0.135 462 Planarity : 0.002 0.009 438 Dihedral : 13.109 75.868 468 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.94 % Favored : 85.06 % Rotamer: Outliers : 5.95 % Allowed : 7.94 % Favored : 86.11 % 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: -2.26 (0.47), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS D 50 PHE 0.011 0.003 PHE D 94 TYR 0.003 0.001 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.02301 ( 20) hydrogen bonds : angle 5.49897 ( 60) covalent geometry : bond 0.00522 ( 2700) covalent geometry : angle 0.61077 ( 3690) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 22 time to evaluate : 0.264 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 34 average time/residue: 0.1448 time to fit residues: 6.0270 Evaluate side-chains 37 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 22 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 10 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 0.0070 chunk 34 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.132612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.091475 restraints weight = 3245.117| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.50 r_work: 0.3243 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2700 Z= 0.129 Angle : 0.531 4.183 3690 Z= 0.294 Chirality : 0.052 0.131 462 Planarity : 0.002 0.007 438 Dihedral : 12.647 75.318 468 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.51 % Favored : 86.49 % Rotamer: Outliers : 5.56 % Allowed : 9.13 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.09 (0.47), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS E 50 PHE 0.008 0.002 PHE D 94 TYR 0.004 0.001 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.01958 ( 20) hydrogen bonds : angle 5.46613 ( 60) covalent geometry : bond 0.00289 ( 2700) covalent geometry : angle 0.53121 ( 3690) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 21 time to evaluate : 0.283 Fit side-chains outliers start: 14 outliers final: 14 residues processed: 33 average time/residue: 0.1426 time to fit residues: 5.8094 Evaluate side-chains 35 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 21 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 26 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.129000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.087015 restraints weight = 3293.793| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.53 r_work: 0.3157 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 2700 Z= 0.247 Angle : 0.629 4.412 3690 Z= 0.351 Chirality : 0.054 0.135 462 Planarity : 0.002 0.009 438 Dihedral : 13.030 75.708 468 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.95 % Favored : 83.05 % Rotamer: Outliers : 6.35 % Allowed : 8.73 % Favored : 84.92 % 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: -2.26 (0.47), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS F 50 PHE 0.012 0.003 PHE D 94 TYR 0.003 0.001 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.02447 ( 20) hydrogen bonds : angle 5.48470 ( 60) covalent geometry : bond 0.00569 ( 2700) covalent geometry : angle 0.62880 ( 3690) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 24 time to evaluate : 0.262 Fit side-chains REVERT: E 43 LYS cc_start: 0.7794 (ptpp) cc_final: 0.7519 (ptpp) outliers start: 16 outliers final: 16 residues processed: 35 average time/residue: 0.1570 time to fit residues: 6.6415 Evaluate side-chains 40 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 24 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 0.0670 chunk 35 optimal weight: 10.0000 chunk 14 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.136425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.095884 restraints weight = 3162.007| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.47 r_work: 0.3378 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2700 Z= 0.078 Angle : 0.468 4.024 3690 Z= 0.259 Chirality : 0.052 0.129 462 Planarity : 0.001 0.006 438 Dihedral : 12.142 74.774 468 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.51 % Favored : 86.49 % Rotamer: Outliers : 3.17 % Allowed : 11.90 % Favored : 84.92 % 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: -1.95 (0.48), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 50 PHE 0.005 0.001 PHE D 94 TYR 0.006 0.001 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.01860 ( 20) hydrogen bonds : angle 5.46713 ( 60) covalent geometry : bond 0.00160 ( 2700) covalent geometry : angle 0.46795 ( 3690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2228.18 seconds wall clock time: 39 minutes 16.59 seconds (2356.59 seconds total)