Starting phenix.real_space_refine on Mon Jan 13 14:49:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zwk_60530/01_2025/8zwk_60530.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zwk_60530/01_2025/8zwk_60530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zwk_60530/01_2025/8zwk_60530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zwk_60530/01_2025/8zwk_60530.map" model { file = "/net/cci-nas-00/data/ceres_data/8zwk_60530/01_2025/8zwk_60530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zwk_60530/01_2025/8zwk_60530.cif" } resolution = 3.4 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: 4 Type Number sf(0) Gaussians P 6 5.49 5 C 1704 2.51 5 N 486 2.21 5 O 564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 2760 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "G" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Restraints were copied for chains: Q, C, B, E, D, F Time building chain proxies: 2.10, per 1000 atoms: 0.76 Number of scatterers: 2760 At special positions: 0 Unit cell: (104.58, 97.11, 32.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 6 15.00 O 564 8.00 N 486 7.00 C 1704 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: 0.68 Conformation dependent library (CDL) restraints added in 354.7 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 28.6% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 45 through 49 removed outlier: 6.803A pdb=" N GLU D 46 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY A 47 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLU A 46 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N VAL E 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL A 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 52 through 54 removed outlier: 6.518A pdb=" N ALA A 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 61 through 62 removed outlier: 6.541A pdb=" N GLU A 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 65 through 66 removed outlier: 6.884A pdb=" N ASN A 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.613A pdb=" N VAL A 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 74 through 82 removed outlier: 6.933A pdb=" N THR D 75 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA A 76 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N THR A 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N ALA E 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N LYS E 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN A 79 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N VAL E 82 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR A 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 49 removed outlier: 6.804A pdb=" N GLU C 46 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY B 47 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLU B 46 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N VAL F 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL B 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 52 through 54 removed outlier: 6.518A pdb=" N ALA B 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 61 through 62 removed outlier: 6.541A pdb=" N GLU B 61 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 65 through 66 removed outlier: 6.885A pdb=" N ASN B 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 69 through 71 removed outlier: 6.613A pdb=" N VAL B 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 74 through 82 removed outlier: 6.932A pdb=" N THR C 75 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA B 76 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N THR B 75 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N ALA F 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL B 77 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N LYS F 80 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN B 79 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N VAL F 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR B 81 " --> pdb=" O VAL F 82 " (cutoff:3.500A) 28 hydrogen bonds defined for protein. 84 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 0.62 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.30: 462 1.30 - 1.38: 516 1.38 - 1.46: 365 1.46 - 1.53: 1315 1.53 - 1.61: 130 Bond restraints: 2788 Sorted by residual: bond pdb=" N GLY F 68 " pdb=" CA GLY F 68 " ideal model delta sigma weight residual 1.445 1.450 -0.006 8.30e-03 1.45e+04 4.68e-01 bond pdb=" N GLY E 68 " pdb=" CA GLY E 68 " ideal model delta sigma weight residual 1.445 1.450 -0.005 8.30e-03 1.45e+04 3.84e-01 bond pdb=" N GLY B 68 " pdb=" CA GLY B 68 " ideal model delta sigma weight residual 1.445 1.450 -0.005 8.30e-03 1.45e+04 3.63e-01 bond pdb=" N GLY C 68 " pdb=" CA GLY C 68 " ideal model delta sigma weight residual 1.445 1.449 -0.005 8.30e-03 1.45e+04 3.47e-01 bond pdb=" N GLY D 68 " pdb=" CA GLY D 68 " ideal model delta sigma weight residual 1.445 1.449 -0.005 8.30e-03 1.45e+04 3.27e-01 ... (remaining 2783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.79: 3303 0.79 - 1.58: 355 1.58 - 2.37: 101 2.37 - 3.16: 25 3.16 - 3.95: 12 Bond angle restraints: 3796 Sorted by residual: angle pdb=" N SER D 42 " pdb=" CA SER D 42 " pdb=" C SER D 42 " ideal model delta sigma weight residual 110.80 114.75 -3.95 2.13e+00 2.20e-01 3.44e+00 angle pdb=" N SER C 42 " pdb=" CA SER C 42 " pdb=" C SER C 42 " ideal model delta sigma weight residual 110.80 114.74 -3.94 2.13e+00 2.20e-01 3.42e+00 angle pdb=" N SER B 42 " pdb=" CA SER B 42 " pdb=" C SER B 42 " ideal model delta sigma weight residual 110.80 114.74 -3.94 2.13e+00 2.20e-01 3.42e+00 angle pdb=" N SER A 42 " pdb=" CA SER A 42 " pdb=" C SER A 42 " ideal model delta sigma weight residual 110.80 114.74 -3.94 2.13e+00 2.20e-01 3.41e+00 angle pdb=" N SER E 42 " pdb=" CA SER E 42 " pdb=" C SER E 42 " ideal model delta sigma weight residual 110.80 114.72 -3.92 2.13e+00 2.20e-01 3.39e+00 ... (remaining 3791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.43: 1550 24.43 - 48.86: 46 48.86 - 73.29: 12 73.29 - 97.71: 0 97.71 - 122.14: 6 Dihedral angle restraints: 1614 sinusoidal: 588 harmonic: 1026 Sorted by residual: dihedral pdb=" CA GLY A 41 " pdb=" C GLY A 41 " pdb=" N SER A 42 " pdb=" CA SER A 42 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLY F 41 " pdb=" C GLY F 41 " pdb=" N SER F 42 " pdb=" CA SER F 42 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLY E 41 " pdb=" C GLY E 41 " pdb=" N SER E 42 " pdb=" CA SER E 42 " ideal model delta harmonic sigma weight residual -180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 1611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 263 0.027 - 0.054: 112 0.054 - 0.081: 51 0.081 - 0.108: 37 0.108 - 0.135: 35 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA VAL D 49 " pdb=" N VAL D 49 " pdb=" C VAL D 49 " pdb=" CB VAL D 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 495 not shown) Planarity restraints: 450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 43 " -0.003 2.00e-02 2.50e+03 6.65e-03 4.42e-01 pdb=" C LYS F 43 " 0.012 2.00e-02 2.50e+03 pdb=" O LYS F 43 " -0.004 2.00e-02 2.50e+03 pdb=" N THR F 44 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 43 " -0.003 2.00e-02 2.50e+03 6.62e-03 4.38e-01 pdb=" C LYS B 43 " 0.011 2.00e-02 2.50e+03 pdb=" O LYS B 43 " -0.004 2.00e-02 2.50e+03 pdb=" N THR B 44 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 43 " 0.003 2.00e-02 2.50e+03 6.61e-03 4.37e-01 pdb=" C LYS A 43 " -0.011 2.00e-02 2.50e+03 pdb=" O LYS A 43 " 0.004 2.00e-02 2.50e+03 pdb=" N THR A 44 " 0.004 2.00e-02 2.50e+03 ... (remaining 447 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 527 2.78 - 3.31: 2457 3.31 - 3.84: 4297 3.84 - 4.37: 4504 4.37 - 4.90: 9330 Nonbonded interactions: 21115 Sorted by model distance: nonbonded pdb=" OE2 GLU C 46 " pdb=" NZ LYS C 80 " model vdw 2.253 3.120 nonbonded pdb=" OE2 GLU F 46 " pdb=" NZ LYS F 80 " model vdw 2.253 3.120 nonbonded pdb=" OE2 GLU D 46 " pdb=" NZ LYS D 80 " model vdw 2.253 3.120 nonbonded pdb=" OE2 GLU E 46 " pdb=" NZ LYS E 80 " model vdw 2.254 3.120 nonbonded pdb=" OE2 GLU A 46 " pdb=" NZ LYS A 80 " model vdw 2.254 3.120 ... (remaining 21110 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 'G' selection = chain 'Q' } 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: 2.300 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: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.730 Find NCS groups from input model: 0.050 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 : 0.003 0.016 2788 Z= 0.219 Angle : 0.602 3.950 3796 Z= 0.340 Chirality : 0.052 0.135 498 Planarity : 0.002 0.007 450 Dihedral : 16.324 122.139 966 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % 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: -5.39 (0.27), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.10 (0.21), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 50 PHE 0.003 0.001 PHE F 94 TYR 0.011 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.262 Fit side-chains REVERT: A 83 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7257 (tp30) REVERT: D 83 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7523 (tp30) REVERT: E 83 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7494 (tp30) REVERT: B 37 VAL cc_start: 0.6552 (m) cc_final: 0.6225 (m) REVERT: B 43 LYS cc_start: 0.6199 (ptpt) cc_final: 0.5442 (tttp) REVERT: B 83 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7353 (tp30) REVERT: F 83 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7593 (tp30) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1722 time to fit residues: 7.3899 Evaluate side-chains 26 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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: 9.9990 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.0270 overall best weight: 2.2044 ------------------------------------------------------------------------------- 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 = 0.4482 r_free = 0.4482 target = 0.179924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.139703 restraints weight = 2749.232| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 2.38 r_work: 0.3949 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3836 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2788 Z= 0.233 Angle : 0.613 4.803 3796 Z= 0.335 Chirality : 0.052 0.128 498 Planarity : 0.002 0.009 450 Dihedral : 15.369 112.539 444 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 5.56 % Allowed : 7.41 % Favored : 87.04 % 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: -4.66 (0.30), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS B 50 PHE 0.011 0.003 PHE A 94 TYR 0.013 0.003 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 19 time to evaluate : 0.271 Fit side-chains REVERT: A 83 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7606 (tp30) REVERT: D 83 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7871 (tp30) REVERT: E 60 LYS cc_start: 0.7351 (mttt) cc_final: 0.6938 (mtpt) REVERT: E 83 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7774 (tp30) REVERT: B 37 VAL cc_start: 0.6978 (OUTLIER) cc_final: 0.6596 (m) REVERT: F 60 LYS cc_start: 0.7316 (mttt) cc_final: 0.6922 (mtpt) REVERT: F 83 GLU cc_start: 0.8540 (mt-10) cc_final: 0.7983 (tp30) outliers start: 15 outliers final: 14 residues processed: 33 average time/residue: 0.1919 time to fit residues: 7.6331 Evaluate side-chains 34 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 19 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 0.0980 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 0.4980 chunk 2 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4537 r_free = 0.4537 target = 0.185882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.143868 restraints weight = 2618.923| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 2.34 r_work: 0.4016 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2788 Z= 0.152 Angle : 0.514 4.251 3796 Z= 0.279 Chirality : 0.049 0.131 498 Planarity : 0.002 0.007 450 Dihedral : 14.367 106.149 444 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 5.19 % Allowed : 8.15 % Favored : 86.67 % 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: -4.36 (0.32), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.24), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.009 0.002 PHE A 94 TYR 0.008 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 19 time to evaluate : 0.288 Fit side-chains REVERT: A 37 VAL cc_start: 0.6791 (OUTLIER) cc_final: 0.6380 (m) REVERT: A 83 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7634 (tp30) REVERT: D 83 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7919 (tp30) REVERT: E 83 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7753 (tp30) REVERT: B 37 VAL cc_start: 0.6944 (OUTLIER) cc_final: 0.6578 (m) REVERT: F 83 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8047 (tp30) outliers start: 14 outliers final: 11 residues processed: 30 average time/residue: 0.1852 time to fit residues: 6.7700 Evaluate side-chains 31 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 18 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 7 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 0.0170 chunk 5 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.0000 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.2028 ------------------------------------------------------------------------------- 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 = 0.4554 r_free = 0.4554 target = 0.188768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.146101 restraints weight = 2603.405| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 2.34 r_work: 0.4024 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3920 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2788 Z= 0.145 Angle : 0.497 4.010 3796 Z= 0.272 Chirality : 0.049 0.131 498 Planarity : 0.002 0.007 450 Dihedral : 13.542 101.070 444 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 6.30 % Allowed : 7.41 % Favored : 86.30 % 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: -3.94 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 50 PHE 0.008 0.002 PHE A 94 TYR 0.008 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 19 time to evaluate : 0.266 Fit side-chains REVERT: A 37 VAL cc_start: 0.6959 (OUTLIER) cc_final: 0.6517 (m) REVERT: D 83 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7982 (tp30) REVERT: E 83 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7923 (tp30) REVERT: B 37 VAL cc_start: 0.7014 (OUTLIER) cc_final: 0.6644 (m) REVERT: F 60 LYS cc_start: 0.7291 (mttt) cc_final: 0.6843 (mtpt) REVERT: F 83 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8050 (tp30) outliers start: 17 outliers final: 12 residues processed: 33 average time/residue: 0.1621 time to fit residues: 6.4953 Evaluate side-chains 32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 18 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 0.0870 chunk 22 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 1 optimal weight: 0.0870 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- 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 = 0.4609 r_free = 0.4609 target = 0.194790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.151535 restraints weight = 2477.864| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.34 r_work: 0.3914 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3804 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 2788 Z= 0.090 Angle : 0.442 3.727 3796 Z= 0.242 Chirality : 0.048 0.131 498 Planarity : 0.001 0.006 450 Dihedral : 13.034 99.443 444 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 4.07 % Allowed : 10.37 % Favored : 85.56 % 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: -3.59 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.006 0.001 PHE A 94 TYR 0.005 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.280 Fit side-chains REVERT: A 37 VAL cc_start: 0.6624 (OUTLIER) cc_final: 0.6171 (m) REVERT: D 83 GLU cc_start: 0.8482 (mt-10) cc_final: 0.7874 (tp30) REVERT: E 83 GLU cc_start: 0.8536 (mt-10) cc_final: 0.7844 (tp30) REVERT: C 37 VAL cc_start: 0.7316 (OUTLIER) cc_final: 0.7016 (m) REVERT: F 83 GLU cc_start: 0.8483 (mt-10) cc_final: 0.7990 (tp30) outliers start: 11 outliers final: 6 residues processed: 28 average time/residue: 0.1730 time to fit residues: 5.9085 Evaluate side-chains 28 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 37 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.176731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.132510 restraints weight = 2731.816| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.44 r_work: 0.3703 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 2788 Z= 0.415 Angle : 0.690 4.313 3796 Z= 0.386 Chirality : 0.052 0.131 498 Planarity : 0.003 0.012 450 Dihedral : 13.201 95.190 444 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 7.41 % Allowed : 8.15 % Favored : 84.44 % 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: -3.78 (0.36), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.005 HIS A 50 PHE 0.016 0.004 PHE A 94 TYR 0.014 0.004 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 30 time to evaluate : 0.271 Fit side-chains REVERT: A 37 VAL cc_start: 0.6861 (OUTLIER) cc_final: 0.6451 (m) REVERT: A 60 LYS cc_start: 0.6660 (mttt) cc_final: 0.6313 (mtpt) REVERT: D 60 LYS cc_start: 0.6537 (mttt) cc_final: 0.6144 (mtpt) REVERT: D 83 GLU cc_start: 0.8538 (mt-10) cc_final: 0.7931 (tp30) REVERT: E 60 LYS cc_start: 0.7195 (mttt) cc_final: 0.6835 (mtpt) REVERT: E 83 GLU cc_start: 0.8678 (mt-10) cc_final: 0.7992 (tp30) REVERT: B 37 VAL cc_start: 0.7073 (OUTLIER) cc_final: 0.6657 (m) REVERT: B 60 LYS cc_start: 0.6631 (mttt) cc_final: 0.6294 (mtpt) REVERT: C 37 VAL cc_start: 0.7287 (OUTLIER) cc_final: 0.7053 (m) REVERT: C 60 LYS cc_start: 0.6678 (mttt) cc_final: 0.6317 (mtpt) REVERT: F 60 LYS cc_start: 0.7309 (mttt) cc_final: 0.6850 (mtpt) REVERT: F 83 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8024 (tp30) outliers start: 20 outliers final: 15 residues processed: 44 average time/residue: 0.1885 time to fit residues: 9.6321 Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 30 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 0.0270 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 0.0570 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- 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 = 0.4586 r_free = 0.4586 target = 0.190379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.145906 restraints weight = 2577.972| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.40 r_work: 0.3860 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2788 Z= 0.105 Angle : 0.469 3.880 3796 Z= 0.257 Chirality : 0.048 0.129 498 Planarity : 0.002 0.006 450 Dihedral : 12.763 96.466 444 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.81 % Allowed : 11.85 % Favored : 83.33 % 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: -3.47 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.008 0.002 PHE E 94 TYR 0.005 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 22 time to evaluate : 0.294 Fit side-chains REVERT: A 37 VAL cc_start: 0.6536 (OUTLIER) cc_final: 0.6092 (m) REVERT: D 83 GLU cc_start: 0.8510 (mt-10) cc_final: 0.7901 (tp30) REVERT: E 60 LYS cc_start: 0.7120 (mttt) cc_final: 0.6730 (mtpt) REVERT: E 83 GLU cc_start: 0.8568 (mt-10) cc_final: 0.7953 (tp30) REVERT: B 37 VAL cc_start: 0.6663 (OUTLIER) cc_final: 0.6225 (m) REVERT: C 37 VAL cc_start: 0.7292 (OUTLIER) cc_final: 0.7001 (m) REVERT: F 60 LYS cc_start: 0.7180 (mttt) cc_final: 0.6738 (mtpt) REVERT: F 83 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8018 (tp30) outliers start: 13 outliers final: 9 residues processed: 30 average time/residue: 0.2126 time to fit residues: 7.5542 Evaluate side-chains 33 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 21 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.4627 r_free = 0.4627 target = 0.193989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.145955 restraints weight = 2555.758| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 2.46 r_work: 0.4056 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3945 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2788 Z= 0.186 Angle : 0.506 3.945 3796 Z= 0.278 Chirality : 0.048 0.126 498 Planarity : 0.002 0.006 450 Dihedral : 12.679 94.803 444 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 5.56 % Allowed : 11.48 % Favored : 82.96 % 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: -3.48 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.010 0.002 PHE A 94 TYR 0.010 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 0.298 Fit side-chains REVERT: A 37 VAL cc_start: 0.6940 (OUTLIER) cc_final: 0.6505 (m) REVERT: A 60 LYS cc_start: 0.6960 (mttt) cc_final: 0.6563 (mtpt) REVERT: D 60 LYS cc_start: 0.6899 (mttt) cc_final: 0.6511 (mtpt) REVERT: E 60 LYS cc_start: 0.7341 (mttt) cc_final: 0.6981 (mtpt) REVERT: B 37 VAL cc_start: 0.6856 (OUTLIER) cc_final: 0.6475 (m) REVERT: B 60 LYS cc_start: 0.6886 (mttt) cc_final: 0.6551 (mtpt) REVERT: C 60 LYS cc_start: 0.7035 (mttt) cc_final: 0.6643 (mtpt) REVERT: F 60 LYS cc_start: 0.7352 (mttt) cc_final: 0.6911 (mtpt) REVERT: F 83 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8110 (tp30) outliers start: 15 outliers final: 12 residues processed: 37 average time/residue: 0.2213 time to fit residues: 9.5170 Evaluate side-chains 39 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 28 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 26 optimal weight: 0.0060 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- 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 = 0.4621 r_free = 0.4621 target = 0.193458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.144954 restraints weight = 2549.475| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 2.50 r_work: 0.4036 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3923 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2788 Z= 0.188 Angle : 0.510 3.937 3796 Z= 0.279 Chirality : 0.049 0.126 498 Planarity : 0.002 0.006 450 Dihedral : 12.573 93.530 444 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 5.19 % Allowed : 12.22 % Favored : 82.59 % 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: -3.49 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.003 HIS B 50 PHE 0.012 0.003 PHE B 94 TYR 0.010 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.279 Fit side-chains REVERT: A 37 VAL cc_start: 0.6917 (OUTLIER) cc_final: 0.6492 (m) REVERT: A 60 LYS cc_start: 0.6868 (mttt) cc_final: 0.6487 (mtpt) REVERT: D 60 LYS cc_start: 0.6861 (mttt) cc_final: 0.6473 (mtpt) REVERT: E 60 LYS cc_start: 0.7299 (mttt) cc_final: 0.6962 (mtpt) REVERT: B 37 VAL cc_start: 0.6883 (OUTLIER) cc_final: 0.6503 (m) REVERT: B 60 LYS cc_start: 0.6793 (mttt) cc_final: 0.6452 (mtpt) REVERT: C 60 LYS cc_start: 0.6909 (mttt) cc_final: 0.6540 (mtpt) REVERT: F 60 LYS cc_start: 0.7298 (mttt) cc_final: 0.6860 (mtpt) REVERT: F 83 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8124 (tp30) outliers start: 14 outliers final: 12 residues processed: 37 average time/residue: 0.2204 time to fit residues: 9.5083 Evaluate side-chains 39 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 0.0980 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4655 r_free = 0.4655 target = 0.197150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.148791 restraints weight = 2534.578| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.44 r_work: 0.4083 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3968 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2788 Z= 0.154 Angle : 0.481 3.829 3796 Z= 0.264 Chirality : 0.048 0.126 498 Planarity : 0.002 0.006 450 Dihedral : 12.415 92.772 444 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 5.56 % Allowed : 11.11 % Favored : 83.33 % 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: -3.47 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.010 0.002 PHE A 94 TYR 0.007 0.002 TYR E 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 26 time to evaluate : 0.369 Fit side-chains REVERT: A 37 VAL cc_start: 0.6905 (OUTLIER) cc_final: 0.6482 (m) REVERT: A 60 LYS cc_start: 0.6876 (mttt) cc_final: 0.6497 (mtpt) REVERT: D 60 LYS cc_start: 0.6930 (mttt) cc_final: 0.6493 (mtpt) REVERT: E 60 LYS cc_start: 0.7281 (mttt) cc_final: 0.6939 (mtpt) REVERT: E 79 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: B 37 VAL cc_start: 0.6927 (OUTLIER) cc_final: 0.6531 (m) REVERT: B 60 LYS cc_start: 0.6821 (mttt) cc_final: 0.6479 (mtpt) REVERT: C 60 LYS cc_start: 0.6934 (mttt) cc_final: 0.6580 (mtpt) REVERT: F 60 LYS cc_start: 0.7303 (mttt) cc_final: 0.6871 (mtpt) REVERT: F 83 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8118 (tp30) outliers start: 15 outliers final: 12 residues processed: 38 average time/residue: 0.2154 time to fit residues: 9.5595 Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 26 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.4656 r_free = 0.4656 target = 0.197120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.148798 restraints weight = 2470.230| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 2.42 r_work: 0.4074 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3966 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2788 Z= 0.155 Angle : 0.480 3.769 3796 Z= 0.263 Chirality : 0.048 0.125 498 Planarity : 0.002 0.006 450 Dihedral : 12.338 92.121 444 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 5.56 % Allowed : 11.11 % Favored : 83.33 % 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: -3.46 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.010 0.003 PHE A 94 TYR 0.009 0.002 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1931.16 seconds wall clock time: 35 minutes 12.16 seconds (2112.16 seconds total)