Starting phenix.real_space_refine on Fri Dec 27 05:12:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xo0_33332/12_2024/7xo0_33332.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo0_33332/12_2024/7xo0_33332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xo0_33332/12_2024/7xo0_33332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo0_33332/12_2024/7xo0_33332.map" model { file = "/net/cci-nas-00/data/ceres_data/7xo0_33332/12_2024/7xo0_33332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo0_33332/12_2024/7xo0_33332.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1602 2.51 5 N 444 2.21 5 O 504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 2550 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "B" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "C" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "E" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "D" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "F" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Time building chain proxies: 2.27, per 1000 atoms: 0.89 Number of scatterers: 2550 At special positions: 0 Unit cell: (92.22, 91.16, 33.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 504 8.00 N 444 7.00 C 1602 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: 0.57 Conformation dependent library (CDL) restraints added in 389.8 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 43.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 37 through 43 removed outlier: 6.605A pdb=" N VAL A 37 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL D 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR A 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N SER D 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY A 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 48 through 55 removed outlier: 6.934A pdb=" N VAL C 52 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA A 53 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR C 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A 55 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY D 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N HIS A 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA D 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N VAL A 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 10.592A pdb=" N VAL D 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N THR A 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 61 through 68 removed outlier: 6.156A pdb=" N GLU A 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR D 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL A 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL D 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASN A 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLY D 68 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N GLY A 67 " --> pdb=" O GLY D 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 71 through 72 removed outlier: 6.310A pdb=" N VAL A 71 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 79 removed outlier: 6.641A pdb=" N VAL A 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.598A pdb=" N VAL A 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.417A pdb=" N ILE A 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 95 through 96 removed outlier: 6.512A pdb=" N VAL A 95 " --> pdb=" O LYS C 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 37 through 43 removed outlier: 6.589A pdb=" N VAL B 37 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL F 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TYR B 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER F 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY B 41 " --> pdb=" O SER F 42 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 48 through 55 removed outlier: 6.940A pdb=" N VAL E 52 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA B 53 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR E 54 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL B 55 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY F 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N HIS B 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA F 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N VAL B 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 10.570A pdb=" N VAL F 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N THR B 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 61 through 68 removed outlier: 6.157A pdb=" N GLU B 61 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N THR F 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL F 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASN B 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLY F 68 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLY B 67 " --> pdb=" O GLY F 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 71 through 72 removed outlier: 6.306A pdb=" N VAL B 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 77 through 79 removed outlier: 6.651A pdb=" N VAL B 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 82 through 83 removed outlier: 6.628A pdb=" N VAL B 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 87 through 89 removed outlier: 6.425A pdb=" N ILE B 88 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.541A pdb=" N VAL B 95 " --> pdb=" O LYS E 96 " (cutoff:3.500A) 46 hydrogen bonds defined for protein. 138 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.62 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 438 1.29 - 1.35: 402 1.35 - 1.42: 102 1.42 - 1.48: 420 1.48 - 1.55: 1200 Bond restraints: 2562 Sorted by residual: bond pdb=" CA VAL F 70 " pdb=" CB VAL F 70 " ideal model delta sigma weight residual 1.533 1.540 -0.008 1.20e-02 6.94e+03 3.97e-01 bond pdb=" CA VAL D 70 " pdb=" CB VAL D 70 " ideal model delta sigma weight residual 1.533 1.540 -0.007 1.20e-02 6.94e+03 3.62e-01 bond pdb=" CA VAL C 70 " pdb=" CB VAL C 70 " ideal model delta sigma weight residual 1.533 1.539 -0.007 1.20e-02 6.94e+03 3.03e-01 bond pdb=" CA LYS E 43 " pdb=" C LYS E 43 " ideal model delta sigma weight residual 1.526 1.531 -0.006 1.08e-02 8.57e+03 2.80e-01 bond pdb=" CA VAL A 70 " pdb=" CB VAL A 70 " ideal model delta sigma weight residual 1.533 1.539 -0.006 1.20e-02 6.94e+03 2.71e-01 ... (remaining 2557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.45: 2818 0.45 - 0.89: 480 0.89 - 1.34: 128 1.34 - 1.79: 24 1.79 - 2.23: 12 Bond angle restraints: 3462 Sorted by residual: angle pdb=" N VAL C 74 " pdb=" CA VAL C 74 " pdb=" C VAL C 74 " ideal model delta sigma weight residual 112.35 110.49 1.86 1.41e+00 5.03e-01 1.74e+00 angle pdb=" N VAL F 74 " pdb=" CA VAL F 74 " pdb=" C VAL F 74 " ideal model delta sigma weight residual 112.35 110.51 1.84 1.41e+00 5.03e-01 1.71e+00 angle pdb=" N VAL D 74 " pdb=" CA VAL D 74 " pdb=" C VAL D 74 " ideal model delta sigma weight residual 112.35 110.51 1.84 1.41e+00 5.03e-01 1.70e+00 angle pdb=" N VAL A 74 " pdb=" CA VAL A 74 " pdb=" C VAL A 74 " ideal model delta sigma weight residual 112.35 110.51 1.84 1.41e+00 5.03e-01 1.70e+00 angle pdb=" N VAL E 74 " pdb=" CA VAL E 74 " pdb=" C VAL E 74 " ideal model delta sigma weight residual 112.35 110.51 1.84 1.41e+00 5.03e-01 1.70e+00 ... (remaining 3457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.00: 1260 12.00 - 23.99: 108 23.99 - 35.98: 66 35.98 - 47.98: 18 47.98 - 59.97: 36 Dihedral angle restraints: 1488 sinusoidal: 492 harmonic: 996 Sorted by residual: dihedral pdb=" CG LYS F 58 " pdb=" CD LYS F 58 " pdb=" CE LYS F 58 " pdb=" NZ LYS F 58 " ideal model delta sinusoidal sigma weight residual 180.00 122.87 57.13 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CG LYS B 58 " pdb=" CD LYS B 58 " pdb=" CE LYS B 58 " pdb=" NZ LYS B 58 " ideal model delta sinusoidal sigma weight residual 180.00 122.87 57.13 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CG LYS D 58 " pdb=" CD LYS D 58 " pdb=" CE LYS D 58 " pdb=" NZ LYS D 58 " ideal model delta sinusoidal sigma weight residual 180.00 122.88 57.12 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 1485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 236 0.025 - 0.050: 126 0.050 - 0.075: 12 0.075 - 0.100: 21 0.100 - 0.124: 61 Chirality restraints: 456 Sorted by residual: chirality pdb=" CA ILE D 88 " pdb=" N ILE D 88 " pdb=" C ILE D 88 " pdb=" CB ILE D 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ILE C 88 " pdb=" N ILE C 88 " pdb=" C ILE C 88 " pdb=" CB ILE C 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 453 not shown) Planarity restraints: 426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 73 " 0.002 2.00e-02 2.50e+03 4.16e-03 1.73e-01 pdb=" C GLY C 73 " -0.007 2.00e-02 2.50e+03 pdb=" O GLY C 73 " 0.003 2.00e-02 2.50e+03 pdb=" N VAL C 74 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 73 " 0.002 2.00e-02 2.50e+03 4.12e-03 1.70e-01 pdb=" C GLY D 73 " -0.007 2.00e-02 2.50e+03 pdb=" O GLY D 73 " 0.003 2.00e-02 2.50e+03 pdb=" N VAL D 74 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 73 " -0.002 2.00e-02 2.50e+03 4.11e-03 1.69e-01 pdb=" C GLY E 73 " 0.007 2.00e-02 2.50e+03 pdb=" O GLY E 73 " -0.003 2.00e-02 2.50e+03 pdb=" N VAL E 74 " -0.002 2.00e-02 2.50e+03 ... (remaining 423 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 536 2.80 - 3.33: 1921 3.33 - 3.85: 4042 3.85 - 4.38: 4053 4.38 - 4.90: 8187 Nonbonded interactions: 18739 Sorted by model distance: nonbonded pdb=" ND2 ASN A 65 " pdb=" OG1 THR C 92 " model vdw 2.280 3.120 nonbonded pdb=" OG1 THR A 92 " pdb=" ND2 ASN D 65 " model vdw 2.283 3.120 nonbonded pdb=" OG1 THR B 92 " pdb=" ND2 ASN F 65 " model vdw 2.283 3.120 nonbonded pdb=" ND2 ASN B 65 " pdb=" OG1 THR E 92 " model vdw 2.292 3.120 nonbonded pdb=" O ALA A 90 " pdb=" ND2 ASN D 65 " model vdw 2.301 3.120 ... (remaining 18734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.480 Find NCS groups from input model: 0.090 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:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 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 : 0.001 0.010 2562 Z= 0.096 Angle : 0.392 2.232 3462 Z= 0.243 Chirality : 0.050 0.124 456 Planarity : 0.001 0.004 426 Dihedral : 16.618 59.972 864 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.001 0.000 PHE E 94 TYR 0.003 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: D 58 LYS cc_start: 0.8584 (mttt) cc_final: 0.8380 (mttm) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 1.6728 time to fit residues: 32.7090 Evaluate side-chains 15 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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: 0.0060 chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2562 Z= 0.230 Angle : 0.413 2.729 3462 Z= 0.249 Chirality : 0.053 0.125 456 Planarity : 0.002 0.006 426 Dihedral : 3.886 12.570 372 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.33 % Allowed : 13.18 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.002 0.001 PHE A 94 TYR 0.006 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7179 (tt0) REVERT: E 43 LYS cc_start: 0.8507 (tttt) cc_final: 0.7938 (ttmt) outliers start: 6 outliers final: 2 residues processed: 36 average time/residue: 1.4009 time to fit residues: 51.6439 Evaluate side-chains 32 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain D residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2562 Z= 0.228 Angle : 0.408 2.495 3462 Z= 0.248 Chirality : 0.053 0.125 456 Planarity : 0.002 0.011 426 Dihedral : 3.902 13.100 372 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.71 % Allowed : 14.34 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.004 0.001 PHE C 94 TYR 0.008 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.287 Fit side-chains REVERT: A 46 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7197 (tt0) REVERT: A 97 LYS cc_start: 0.8173 (mmmt) cc_final: 0.7916 (mppt) REVERT: B 97 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7217 (tmtt) REVERT: E 43 LYS cc_start: 0.8476 (tttt) cc_final: 0.7890 (ttmt) REVERT: E 96 LYS cc_start: 0.8739 (tttt) cc_final: 0.8504 (tppp) REVERT: D 58 LYS cc_start: 0.8690 (mttp) cc_final: 0.8462 (mttm) REVERT: F 97 LYS cc_start: 0.7780 (mptp) cc_final: 0.7413 (mppt) outliers start: 7 outliers final: 4 residues processed: 38 average time/residue: 1.2669 time to fit residues: 49.3318 Evaluate side-chains 36 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2562 Z= 0.136 Angle : 0.363 2.421 3462 Z= 0.222 Chirality : 0.052 0.125 456 Planarity : 0.001 0.011 426 Dihedral : 3.723 11.729 372 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.71 % Allowed : 15.50 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.002 0.001 PHE A 94 TYR 0.009 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.291 Fit side-chains REVERT: A 46 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7188 (tt0) REVERT: A 97 LYS cc_start: 0.8188 (mmmt) cc_final: 0.7948 (mppt) REVERT: B 97 LYS cc_start: 0.8024 (mmmt) cc_final: 0.7362 (tmtt) REVERT: E 96 LYS cc_start: 0.8744 (tttt) cc_final: 0.8512 (tppp) REVERT: F 97 LYS cc_start: 0.7800 (mptp) cc_final: 0.7415 (mppt) outliers start: 7 outliers final: 4 residues processed: 41 average time/residue: 1.3234 time to fit residues: 55.5482 Evaluate side-chains 39 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 0.0070 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 0.3980 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 overall best weight: 2.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2562 Z= 0.279 Angle : 0.427 2.526 3462 Z= 0.259 Chirality : 0.054 0.128 456 Planarity : 0.002 0.013 426 Dihedral : 4.013 13.363 372 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.26 % Allowed : 15.12 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.004 0.001 PHE C 94 TYR 0.009 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.279 Fit side-chains REVERT: A 46 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: A 97 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7809 (mppt) REVERT: B 97 LYS cc_start: 0.8010 (mmmt) cc_final: 0.7435 (tmtt) REVERT: E 96 LYS cc_start: 0.8781 (tttt) cc_final: 0.8540 (tppp) REVERT: F 97 LYS cc_start: 0.7740 (mptp) cc_final: 0.7409 (mppt) outliers start: 11 outliers final: 6 residues processed: 45 average time/residue: 1.0882 time to fit residues: 50.3185 Evaluate side-chains 42 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 8.9990 chunk 34 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2562 Z= 0.111 Angle : 0.357 2.362 3462 Z= 0.219 Chirality : 0.052 0.125 456 Planarity : 0.001 0.012 426 Dihedral : 3.715 11.360 372 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.94 % Allowed : 18.99 % Favored : 79.07 % 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: -2.54 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.001 0.000 PHE A 94 TYR 0.006 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.267 Fit side-chains REVERT: A 46 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: A 97 LYS cc_start: 0.7971 (mmmt) cc_final: 0.7718 (mppt) REVERT: B 97 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7483 (tmtt) REVERT: E 96 LYS cc_start: 0.8768 (tttt) cc_final: 0.8535 (tppp) REVERT: F 97 LYS cc_start: 0.7694 (mptp) cc_final: 0.7390 (mppt) outliers start: 5 outliers final: 1 residues processed: 38 average time/residue: 1.2693 time to fit residues: 49.4562 Evaluate side-chains 35 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2562 Z= 0.208 Angle : 0.391 2.404 3462 Z= 0.238 Chirality : 0.053 0.127 456 Planarity : 0.001 0.005 426 Dihedral : 3.877 12.587 372 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.33 % Allowed : 18.99 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.002 0.001 PHE C 94 TYR 0.008 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.276 Fit side-chains REVERT: A 46 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7252 (tt0) REVERT: A 97 LYS cc_start: 0.7977 (mmmt) cc_final: 0.7765 (mppt) REVERT: B 97 LYS cc_start: 0.8079 (mmmt) cc_final: 0.7590 (tmtt) REVERT: E 96 LYS cc_start: 0.8787 (tttt) cc_final: 0.8553 (tppp) REVERT: F 97 LYS cc_start: 0.7695 (mptp) cc_final: 0.7391 (mppt) outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 1.2049 time to fit residues: 48.2382 Evaluate side-chains 39 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2562 Z= 0.375 Angle : 0.478 2.535 3462 Z= 0.288 Chirality : 0.055 0.129 456 Planarity : 0.002 0.014 426 Dihedral : 4.206 14.326 372 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.10 % Allowed : 17.44 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.005 0.001 PHE C 94 TYR 0.010 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.277 Fit side-chains REVERT: A 46 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: B 97 LYS cc_start: 0.8081 (mmmt) cc_final: 0.7653 (tmtt) REVERT: E 96 LYS cc_start: 0.8802 (tttt) cc_final: 0.8559 (tppp) REVERT: F 97 LYS cc_start: 0.7728 (mptp) cc_final: 0.7394 (mppt) outliers start: 8 outliers final: 6 residues processed: 41 average time/residue: 1.1359 time to fit residues: 47.8992 Evaluate side-chains 41 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2562 Z= 0.270 Angle : 0.430 2.517 3462 Z= 0.261 Chirality : 0.054 0.128 456 Planarity : 0.002 0.014 426 Dihedral : 4.125 13.519 372 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.49 % Allowed : 17.83 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.003 0.001 PHE A 94 TYR 0.008 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.273 Fit side-chains REVERT: A 46 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7293 (tt0) REVERT: B 97 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7624 (tmtt) REVERT: E 96 LYS cc_start: 0.8802 (tttt) cc_final: 0.8560 (tppp) REVERT: F 97 LYS cc_start: 0.7728 (mptp) cc_final: 0.7393 (mppt) outliers start: 9 outliers final: 5 residues processed: 40 average time/residue: 1.1934 time to fit residues: 48.9889 Evaluate side-chains 40 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 8 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 28 optimal weight: 0.0980 chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2562 Z= 0.181 Angle : 0.388 3.091 3462 Z= 0.236 Chirality : 0.053 0.127 456 Planarity : 0.002 0.015 426 Dihedral : 3.931 12.525 372 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.33 % Allowed : 18.22 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.002 0.001 PHE C 94 TYR 0.007 0.001 TYR F 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.283 Fit side-chains REVERT: A 46 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7268 (tt0) REVERT: B 97 LYS cc_start: 0.8066 (mmmt) cc_final: 0.7660 (tmtt) REVERT: E 96 LYS cc_start: 0.8796 (tttt) cc_final: 0.8559 (tppp) REVERT: F 97 LYS cc_start: 0.7754 (mptp) cc_final: 0.7419 (mppt) outliers start: 6 outliers final: 4 residues processed: 40 average time/residue: 1.1714 time to fit residues: 48.1257 Evaluate side-chains 38 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 0.0040 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.100489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.089909 restraints weight = 3328.431| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.64 r_work: 0.3053 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2562 Z= 0.221 Angle : 0.405 2.986 3462 Z= 0.246 Chirality : 0.053 0.127 456 Planarity : 0.002 0.015 426 Dihedral : 3.996 12.728 372 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.71 % Allowed : 17.44 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.002 0.001 PHE C 94 TYR 0.011 0.002 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1423.69 seconds wall clock time: 26 minutes 20.76 seconds (1580.76 seconds total)