Starting phenix.real_space_refine on Wed Jun 4 12:17:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zwk_60530/06_2025/8zwk_60530.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zwk_60530/06_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_60530/06_2025/8zwk_60530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zwk_60530/06_2025/8zwk_60530.map" model { file = "/net/cci-nas-00/data/ceres_data/8zwk_60530/06_2025/8zwk_60530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zwk_60530/06_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 2.00, per 1000 atoms: 0.72 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: 0.58 Conformation dependent library (CDL) restraints added in 316.2 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: 0.74 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: 0.55 Time building geometry restraints manager: 0.70 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: 3.320 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: 0.020 Set scattering table: 0.020 Process input model: 11.070 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.280 ------------------------------------------------------------------------------- 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= 0.157 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 Details of bonding type rmsd hydrogen bonds : bond 0.21901 ( 28) hydrogen bonds : angle 8.52070 ( 84) covalent geometry : bond 0.00320 ( 2788) covalent geometry : angle 0.60201 ( 3796) *********************** 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 : 0.253 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: 0.1806 time to fit residues: 7.7082 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 = 37)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.139707 restraints weight = 2749.232| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 2.38 r_work: 0.3953 rms_B_bonded: 2.63 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= 0.158 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 Details of bonding type rmsd hydrogen bonds : bond 0.02219 ( 28) hydrogen bonds : angle 7.20535 ( 84) covalent geometry : bond 0.00341 ( 2788) covalent geometry : angle 0.61271 ( 3796) *********************** 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 : 0.303 Fit side-chains REVERT: A 83 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7602 (tp30) REVERT: D 83 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7869 (tp30) REVERT: E 60 LYS cc_start: 0.7351 (mttt) cc_final: 0.6937 (mtpt) REVERT: E 83 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7772 (tp30) REVERT: B 37 VAL cc_start: 0.6969 (OUTLIER) cc_final: 0.6588 (m) REVERT: F 60 LYS cc_start: 0.7315 (mttt) cc_final: 0.6921 (mtpt) REVERT: F 83 GLU cc_start: 0.8542 (mt-10) cc_final: 0.7982 (tp30) outliers start: 15 outliers final: 14 residues processed: 33 average time/residue: 0.1856 time to fit residues: 7.3910 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 : 0.315 ------------------------------------------------------------------------------- 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: 0.0570 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.8100 ------------------------------------------------------------------------------- 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 = 0.187622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.145688 restraints weight = 2595.582| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 2.38 r_work: 0.4044 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3933 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 2788 Z= 0.083 Angle : 0.487 4.295 3796 Z= 0.266 Chirality : 0.049 0.129 498 Planarity : 0.001 0.007 450 Dihedral : 14.415 106.811 444 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.33 % Allowed : 9.26 % Favored : 87.41 % 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: -4.37 (0.32), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.008 0.002 PHE A 94 TYR 0.006 0.001 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.02256 ( 28) hydrogen bonds : angle 6.80266 ( 84) covalent geometry : bond 0.00161 ( 2788) covalent geometry : angle 0.48727 ( 3796) *********************** 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 28 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.281 Fit side-chains REVERT: A 37 VAL cc_start: 0.6708 (OUTLIER) cc_final: 0.6295 (m) REVERT: A 83 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7643 (tp30) REVERT: D 83 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7911 (tp30) REVERT: B 37 VAL cc_start: 0.6837 (OUTLIER) cc_final: 0.6465 (m) REVERT: F 83 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8010 (tp30) outliers start: 9 outliers final: 6 residues processed: 27 average time/residue: 0.1709 time to fit residues: 5.6589 Evaluate side-chains 27 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 79 GLN 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 79 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 7 optimal weight: 0.0870 chunk 33 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 16 optimal weight: 0.0770 overall best weight: 1.3920 ------------------------------------------------------------------------------- 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 = 0.4546 r_free = 0.4546 target = 0.187213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.144612 restraints weight = 2612.294| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 2.35 r_work: 0.4020 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2788 Z= 0.107 Angle : 0.504 4.054 3796 Z= 0.276 Chirality : 0.049 0.126 498 Planarity : 0.002 0.006 450 Dihedral : 13.818 102.509 444 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 5.93 % Allowed : 6.67 % Favored : 87.41 % 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: -4.01 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 50 PHE 0.007 0.002 PHE A 94 TYR 0.009 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.02192 ( 28) hydrogen bonds : angle 6.72371 ( 84) covalent geometry : bond 0.00230 ( 2788) covalent geometry : angle 0.50361 ( 3796) *********************** 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 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 19 time to evaluate : 0.225 Fit side-chains REVERT: A 37 VAL cc_start: 0.6936 (OUTLIER) cc_final: 0.6500 (m) REVERT: D 83 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7942 (tp30) REVERT: E 83 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7922 (tp30) REVERT: B 37 VAL cc_start: 0.6952 (OUTLIER) cc_final: 0.6583 (m) REVERT: F 60 LYS cc_start: 0.7311 (mttt) cc_final: 0.6851 (mtpt) REVERT: F 83 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8024 (tp30) outliers start: 16 outliers final: 13 residues processed: 33 average time/residue: 0.1444 time to fit residues: 5.7831 Evaluate side-chains 33 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 18 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 0.0010 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.3192 ------------------------------------------------------------------------------- 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 = 0.4559 r_free = 0.4559 target = 0.188466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.144902 restraints weight = 2545.556| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 2.36 r_work: 0.4022 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3913 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2788 Z= 0.102 Angle : 0.483 3.941 3796 Z= 0.265 Chirality : 0.048 0.127 498 Planarity : 0.002 0.006 450 Dihedral : 13.041 98.544 444 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 6.30 % Allowed : 8.52 % Favored : 85.19 % 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: -3.69 (0.37), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 50 PHE 0.009 0.002 PHE B 94 TYR 0.007 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.02168 ( 28) hydrogen bonds : angle 6.64514 ( 84) covalent geometry : bond 0.00217 ( 2788) covalent geometry : angle 0.48317 ( 3796) *********************** 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 37 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 20 time to evaluate : 0.256 Fit side-chains REVERT: A 37 VAL cc_start: 0.6881 (OUTLIER) cc_final: 0.6416 (m) REVERT: D 83 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7959 (tp30) REVERT: E 60 LYS cc_start: 0.7264 (mttt) cc_final: 0.6856 (mtpt) REVERT: B 37 VAL cc_start: 0.6936 (OUTLIER) cc_final: 0.6567 (m) REVERT: F 60 LYS cc_start: 0.7287 (mttt) cc_final: 0.6854 (mtpt) REVERT: F 83 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8039 (tp30) outliers start: 17 outliers final: 13 residues processed: 34 average time/residue: 0.1921 time to fit residues: 7.7126 Evaluate side-chains 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 20 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 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 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 75 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.4447 r_free = 0.4447 target = 0.176108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.131612 restraints weight = 2736.770| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.44 r_work: 0.3853 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3743 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 2788 Z= 0.281 Angle : 0.698 4.315 3796 Z= 0.391 Chirality : 0.052 0.128 498 Planarity : 0.003 0.012 450 Dihedral : 13.234 94.762 444 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 8.52 % Allowed : 7.41 % Favored : 84.07 % 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: -3.92 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.006 HIS A 50 PHE 0.017 0.004 PHE A 94 TYR 0.015 0.004 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 28) hydrogen bonds : angle 7.44458 ( 84) covalent geometry : bond 0.00640 ( 2788) covalent geometry : angle 0.69843 ( 3796) *********************** 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 52 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 29 time to evaluate : 0.263 Fit side-chains REVERT: A 37 VAL cc_start: 0.7032 (OUTLIER) cc_final: 0.6612 (m) REVERT: A 60 LYS cc_start: 0.6899 (mttt) cc_final: 0.6540 (mtpt) REVERT: D 60 LYS cc_start: 0.6746 (mttt) cc_final: 0.6352 (mtpt) REVERT: D 83 GLU cc_start: 0.8503 (mt-10) cc_final: 0.7915 (tp30) REVERT: E 60 LYS cc_start: 0.7294 (mttt) cc_final: 0.6946 (mtpt) REVERT: E 83 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8037 (tp30) REVERT: B 37 VAL cc_start: 0.7195 (OUTLIER) cc_final: 0.6765 (m) REVERT: B 60 LYS cc_start: 0.6848 (mttt) cc_final: 0.6511 (mtpt) REVERT: C 37 VAL cc_start: 0.7383 (OUTLIER) cc_final: 0.7065 (m) REVERT: C 60 LYS cc_start: 0.6870 (mttt) cc_final: 0.6503 (mtpt) REVERT: F 60 LYS cc_start: 0.7403 (mttt) cc_final: 0.6941 (mtpt) REVERT: F 83 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8086 (tp30) outliers start: 23 outliers final: 19 residues processed: 47 average time/residue: 0.1875 time to fit residues: 10.2323 Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 29 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 79 GLN 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 D residue 79 GLN 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 B residue 87 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.4514 r_free = 0.4514 target = 0.182970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.137839 restraints weight = 2673.932| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.50 r_work: 0.3762 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2646 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= 0.141 Angle : 0.535 4.270 3796 Z= 0.293 Chirality : 0.050 0.128 498 Planarity : 0.002 0.007 450 Dihedral : 12.979 95.471 444 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 7.41 % Allowed : 9.63 % 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: -3.75 (0.36), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS B 50 PHE 0.013 0.003 PHE A 94 TYR 0.011 0.002 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.02406 ( 28) hydrogen bonds : angle 7.06245 ( 84) covalent geometry : bond 0.00310 ( 2788) covalent geometry : angle 0.53480 ( 3796) *********************** 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 44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 24 time to evaluate : 0.248 Fit side-chains REVERT: A 37 VAL cc_start: 0.6700 (OUTLIER) cc_final: 0.6259 (m) REVERT: A 60 LYS cc_start: 0.6633 (mttt) cc_final: 0.6235 (mtpt) REVERT: D 60 LYS cc_start: 0.6585 (mttt) cc_final: 0.6187 (mtpt) REVERT: D 83 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7899 (tp30) REVERT: E 60 LYS cc_start: 0.7178 (mttt) cc_final: 0.6822 (mtpt) REVERT: B 37 VAL cc_start: 0.6906 (OUTLIER) cc_final: 0.6542 (m) REVERT: B 60 LYS cc_start: 0.6507 (mttt) cc_final: 0.6174 (mtpt) REVERT: C 60 LYS cc_start: 0.6649 (mttt) cc_final: 0.6289 (mtpt) REVERT: F 60 LYS cc_start: 0.7275 (mttt) cc_final: 0.6825 (mtpt) REVERT: F 83 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8051 (tp30) outliers start: 20 outliers final: 18 residues processed: 41 average time/residue: 0.1955 time to fit residues: 9.2651 Evaluate side-chains 44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 24 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.4593 r_free = 0.4593 target = 0.190337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.142191 restraints weight = 2591.414| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 2.47 r_work: 0.4009 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3899 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2788 Z= 0.143 Angle : 0.542 4.286 3796 Z= 0.298 Chirality : 0.049 0.127 498 Planarity : 0.002 0.007 450 Dihedral : 12.796 93.975 444 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 7.78 % Allowed : 9.26 % 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: -3.66 (0.37), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 50 PHE 0.013 0.003 PHE A 94 TYR 0.012 0.003 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.02436 ( 28) hydrogen bonds : angle 7.01769 ( 84) covalent geometry : bond 0.00312 ( 2788) covalent geometry : angle 0.54174 ( 3796) *********************** 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 45 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 24 time to evaluate : 0.261 Fit side-chains REVERT: A 37 VAL cc_start: 0.6955 (OUTLIER) cc_final: 0.6503 (m) REVERT: A 60 LYS cc_start: 0.6963 (mttt) cc_final: 0.6595 (mtpt) REVERT: D 60 LYS cc_start: 0.6990 (mttt) cc_final: 0.6551 (mtpt) REVERT: E 60 LYS cc_start: 0.7291 (mttt) cc_final: 0.6957 (mtpt) REVERT: B 37 VAL cc_start: 0.7042 (OUTLIER) cc_final: 0.6668 (m) REVERT: B 60 LYS cc_start: 0.6815 (mttt) cc_final: 0.6501 (mtpt) REVERT: C 60 LYS cc_start: 0.7012 (mttt) cc_final: 0.6657 (mtpt) REVERT: F 60 LYS cc_start: 0.7358 (mttt) cc_final: 0.6930 (mtpt) REVERT: F 83 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8106 (tp30) outliers start: 21 outliers final: 18 residues processed: 41 average time/residue: 0.2295 time to fit residues: 10.8814 Evaluate side-chains 44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 24 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 28 optimal weight: 0.2980 chunk 21 optimal weight: 7.9990 chunk 26 optimal weight: 0.4980 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4647 r_free = 0.4647 target = 0.195777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.147212 restraints weight = 2524.445| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.50 r_work: 0.4081 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3974 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2922 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= 0.093 Angle : 0.475 3.914 3796 Z= 0.260 Chirality : 0.049 0.129 498 Planarity : 0.002 0.006 450 Dihedral : 12.493 93.018 444 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 7.04 % Allowed : 10.00 % 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: -3.51 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.009 0.002 PHE A 94 TYR 0.008 0.002 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.02066 ( 28) hydrogen bonds : angle 6.77938 ( 84) covalent geometry : bond 0.00198 ( 2788) covalent geometry : angle 0.47456 ( 3796) *********************** 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 43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 24 time to evaluate : 0.306 Fit side-chains REVERT: A 37 VAL cc_start: 0.6857 (OUTLIER) cc_final: 0.6423 (m) REVERT: A 60 LYS cc_start: 0.6909 (mttt) cc_final: 0.6550 (mtpt) REVERT: D 60 LYS cc_start: 0.6884 (mttt) cc_final: 0.6446 (mtpt) REVERT: E 60 LYS cc_start: 0.7298 (mttt) cc_final: 0.6958 (mtpt) REVERT: B 60 LYS cc_start: 0.6823 (mttt) cc_final: 0.6484 (mtpt) REVERT: C 60 LYS cc_start: 0.6966 (mttt) cc_final: 0.6606 (mtpt) REVERT: F 60 LYS cc_start: 0.7300 (mttt) cc_final: 0.6864 (mtpt) REVERT: F 83 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8082 (tp30) outliers start: 19 outliers final: 16 residues processed: 40 average time/residue: 0.1966 time to fit residues: 9.1657 Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 24 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 79 GLN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.4589 r_free = 0.4589 target = 0.189792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.141279 restraints weight = 2609.668| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 2.48 r_work: 0.3994 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2788 Z= 0.170 Angle : 0.570 4.136 3796 Z= 0.315 Chirality : 0.049 0.126 498 Planarity : 0.002 0.008 450 Dihedral : 12.596 91.467 444 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 6.67 % Allowed : 10.74 % 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: -3.62 (0.37), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 50 PHE 0.015 0.004 PHE A 94 TYR 0.013 0.003 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.02559 ( 28) hydrogen bonds : angle 7.02020 ( 84) covalent geometry : bond 0.00376 ( 2788) covalent geometry : angle 0.57006 ( 3796) ********************** 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 45 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 27 time to evaluate : 0.296 Fit side-chains REVERT: A 37 VAL cc_start: 0.7012 (OUTLIER) cc_final: 0.6584 (m) REVERT: A 60 LYS cc_start: 0.7035 (mttt) cc_final: 0.6652 (mtpt) REVERT: D 60 LYS cc_start: 0.6976 (mttt) cc_final: 0.6555 (mtpt) REVERT: E 60 LYS cc_start: 0.7326 (mttt) cc_final: 0.6989 (mtpt) REVERT: B 37 VAL cc_start: 0.7098 (OUTLIER) cc_final: 0.6725 (m) REVERT: B 60 LYS cc_start: 0.6879 (mttt) cc_final: 0.6567 (mtpt) REVERT: C 60 LYS cc_start: 0.7118 (mttt) cc_final: 0.6753 (mtpt) REVERT: F 60 LYS cc_start: 0.7390 (mttt) cc_final: 0.6961 (mtpt) REVERT: F 83 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8113 (tp30) outliers start: 18 outliers final: 16 residues processed: 40 average time/residue: 0.1908 time to fit residues: 8.8880 Evaluate side-chains 45 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 27 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 79 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.0170 chunk 34 optimal weight: 2.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- 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 = 0.4611 r_free = 0.4611 target = 0.191936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.143178 restraints weight = 2516.429| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 2.49 r_work: 0.4017 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3906 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3067 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= 0.130 Angle : 0.519 4.048 3796 Z= 0.284 Chirality : 0.049 0.128 498 Planarity : 0.002 0.007 450 Dihedral : 12.471 90.995 444 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 6.67 % Allowed : 10.00 % 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: -3.62 (0.37), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.012 0.003 PHE B 94 TYR 0.010 0.002 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.02176 ( 28) hydrogen bonds : angle 6.88170 ( 84) covalent geometry : bond 0.00284 ( 2788) covalent geometry : angle 0.51906 ( 3796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1855.58 seconds wall clock time: 32 minutes 37.14 seconds (1957.14 seconds total)