Starting phenix.real_space_refine on Fri Dec 27 05:13:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ynp_33968/12_2024/7ynp_33968_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ynp_33968/12_2024/7ynp_33968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ynp_33968/12_2024/7ynp_33968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ynp_33968/12_2024/7ynp_33968.map" model { file = "/net/cci-nas-00/data/ceres_data/7ynp_33968/12_2024/7ynp_33968_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ynp_33968/12_2024/7ynp_33968_neut.cif" } resolution = 2.8 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 S 2 5.16 5 C 1620 2.51 5 N 444 2.21 5 O 502 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: 2568 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "D" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'IZM': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: F, C, B, E Time building chain proxies: 2.39, per 1000 atoms: 0.93 Number of scatterers: 2568 At special positions: 0 Unit cell: (97.11, 105.41, 31.54, 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) S 2 16.00 O 502 8.00 N 444 7.00 C 1620 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: 0.64 Conformation dependent library (CDL) restraints added in 342.1 milliseconds 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 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, 41.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 39 through 40 removed outlier: 6.345A pdb=" N TYR A 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 55 removed outlier: 5.724A pdb=" N GLU A 46 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N VAL B 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N GLY B 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N HIS A 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ALA B 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 9.125A pdb=" N VAL A 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N VAL B 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N THR A 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU D 46 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLY A 47 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL D 52 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA A 53 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR D 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A 55 " --> pdb=" O THR D 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 66 removed outlier: 6.350A pdb=" N THR A 64 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 70 through 72 removed outlier: 6.252A pdb=" N VAL A 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 82 removed outlier: 5.988A pdb=" N THR A 75 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N ALA B 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL A 77 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N LYS B 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLN A 79 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N VAL B 82 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR A 81 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA A 76 " --> pdb=" O THR D 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 87 removed outlier: 6.513A pdb=" N GLY A 86 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 91 through 92 removed outlier: 6.561A pdb=" N ALA A 91 " --> pdb=" O THR B 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 95 through 96 removed outlier: 6.415A pdb=" N VAL A 95 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 39 through 40 removed outlier: 6.338A pdb=" N TYR C 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 45 through 55 removed outlier: 5.710A pdb=" N GLU C 46 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N VAL E 49 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL C 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N GLY E 51 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N HIS C 50 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ALA E 53 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N VAL C 52 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N VAL E 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N THR C 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLU F 46 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY C 47 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL F 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA C 53 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR F 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL C 55 " --> pdb=" O THR F 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 64 through 66 removed outlier: 6.358A pdb=" N THR C 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 70 through 72 removed outlier: 6.250A pdb=" N VAL C 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 75 through 82 removed outlier: 5.992A pdb=" N THR C 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ALA E 78 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL C 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N LYS E 80 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLN C 79 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N VAL E 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR C 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA C 76 " --> pdb=" O THR F 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 86 through 87 removed outlier: 6.496A pdb=" N GLY C 86 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 91 through 92 removed outlier: 6.556A pdb=" N ALA C 91 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.390A pdb=" N VAL C 95 " --> pdb=" O LYS F 96 " (cutoff:3.500A) 36 hydrogen bonds defined for protein. 108 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: 0.59 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.30: 432 1.30 - 1.37: 424 1.37 - 1.45: 260 1.45 - 1.53: 1331 1.53 - 1.61: 137 Bond restraints: 2584 Sorted by residual: bond pdb=" C10 IZM D 201 " pdb=" S17 IZM D 201 " ideal model delta sigma weight residual 1.748 1.575 0.173 2.00e-02 2.50e+03 7.46e+01 bond pdb=" C10 IZM F 201 " pdb=" S17 IZM F 201 " ideal model delta sigma weight residual 1.748 1.576 0.172 2.00e-02 2.50e+03 7.40e+01 bond pdb=" C09 IZM D 201 " pdb=" C10 IZM D 201 " ideal model delta sigma weight residual 1.433 1.574 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C09 IZM F 201 " pdb=" C10 IZM F 201 " ideal model delta sigma weight residual 1.433 1.573 -0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" C13 IZM D 201 " pdb=" S17 IZM D 201 " ideal model delta sigma weight residual 1.744 1.608 0.136 2.00e-02 2.50e+03 4.60e+01 ... (remaining 2579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 3413 2.54 - 5.07: 67 5.07 - 7.61: 8 7.61 - 10.14: 4 10.14 - 12.68: 4 Bond angle restraints: 3496 Sorted by residual: angle pdb=" C08 IZM F 201 " pdb=" C09 IZM F 201 " pdb=" C10 IZM F 201 " ideal model delta sigma weight residual 125.57 112.89 12.68 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C08 IZM D 201 " pdb=" C09 IZM D 201 " pdb=" C10 IZM D 201 " ideal model delta sigma weight residual 125.57 112.97 12.60 3.00e+00 1.11e-01 1.76e+01 angle pdb=" C07 IZM F 201 " pdb=" C08 IZM F 201 " pdb=" C09 IZM F 201 " ideal model delta sigma weight residual 123.72 111.56 12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" C07 IZM D 201 " pdb=" C08 IZM D 201 " pdb=" C09 IZM D 201 " ideal model delta sigma weight residual 123.72 111.57 12.15 3.00e+00 1.11e-01 1.64e+01 angle pdb=" C10 IZM F 201 " pdb=" S17 IZM F 201 " pdb=" C13 IZM F 201 " ideal model delta sigma weight residual 89.24 99.25 -10.01 3.00e+00 1.11e-01 1.11e+01 ... (remaining 3491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 1322 16.28 - 32.57: 138 32.57 - 48.85: 30 48.85 - 65.13: 0 65.13 - 81.42: 4 Dihedral angle restraints: 1494 sinusoidal: 504 harmonic: 990 Sorted by residual: dihedral pdb=" CB LYS D 60 " pdb=" CG LYS D 60 " pdb=" CD LYS D 60 " pdb=" CE LYS D 60 " ideal model delta sinusoidal sigma weight residual 180.00 140.70 39.30 3 1.50e+01 4.44e-03 6.96e+00 dihedral pdb=" CB LYS B 60 " pdb=" CG LYS B 60 " pdb=" CD LYS B 60 " pdb=" CE LYS B 60 " ideal model delta sinusoidal sigma weight residual 180.00 140.77 39.23 3 1.50e+01 4.44e-03 6.94e+00 dihedral pdb=" CB LYS A 60 " pdb=" CG LYS A 60 " pdb=" CD LYS A 60 " pdb=" CE LYS A 60 " ideal model delta sinusoidal sigma weight residual 180.00 140.78 39.22 3 1.50e+01 4.44e-03 6.94e+00 ... (remaining 1491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 210 0.032 - 0.064: 134 0.064 - 0.097: 52 0.097 - 0.129: 54 0.129 - 0.161: 6 Chirality restraints: 456 Sorted by residual: chirality pdb=" CB THR D 72 " pdb=" CA THR D 72 " pdb=" OG1 THR D 72 " pdb=" CG2 THR D 72 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CB THR A 72 " pdb=" CA THR A 72 " pdb=" OG1 THR A 72 " pdb=" CG2 THR A 72 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CB THR E 72 " pdb=" CA THR E 72 " pdb=" OG1 THR E 72 " pdb=" CG2 THR E 72 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 453 not shown) Planarity restraints: 428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 50 " 0.009 2.00e-02 2.50e+03 8.58e-03 1.10e+00 pdb=" CG HIS A 50 " -0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS A 50 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS A 50 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS A 50 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS A 50 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 50 " -0.009 2.00e-02 2.50e+03 8.28e-03 1.03e+00 pdb=" CG HIS F 50 " 0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS F 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS F 50 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS F 50 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS F 50 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 50 " -0.009 2.00e-02 2.50e+03 8.24e-03 1.02e+00 pdb=" CG HIS E 50 " 0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS E 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS E 50 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS E 50 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS E 50 " -0.002 2.00e-02 2.50e+03 ... (remaining 425 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 554 2.79 - 3.32: 2084 3.32 - 3.85: 3980 3.85 - 4.37: 4422 4.37 - 4.90: 9044 Nonbonded interactions: 20084 Sorted by model distance: nonbonded pdb=" OE1 GLU D 46 " pdb=" NZ LYS D 80 " model vdw 2.265 3.120 nonbonded pdb=" OE1 GLU E 46 " pdb=" NZ LYS E 80 " model vdw 2.266 3.120 nonbonded pdb=" OE1 GLU F 46 " pdb=" NZ LYS F 80 " model vdw 2.266 3.120 nonbonded pdb=" OE1 GLU C 46 " pdb=" NZ LYS C 80 " model vdw 2.266 3.120 nonbonded pdb=" OE1 GLU A 46 " pdb=" NZ LYS A 80 " model vdw 2.266 3.120 ... (remaining 20079 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' and resid 37 through 97) selection = chain 'E' selection = (chain 'F' and resid 37 through 97) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 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: 0.030 Process input model: 11.570 Find NCS groups from input model: 0.110 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:11.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 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 : 0.012 0.173 2584 Z= 0.766 Angle : 0.965 12.679 3496 Z= 0.479 Chirality : 0.056 0.161 456 Planarity : 0.003 0.009 428 Dihedral : 13.694 81.418 870 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % 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: -3.88 (0.34), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.26), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.005 HIS A 50 PHE 0.012 0.004 PHE D 94 TYR 0.011 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.271 Fit side-chains REVERT: A 62 GLN cc_start: 0.6485 (tt0) cc_final: 0.6228 (tt0) REVERT: C 62 GLN cc_start: 0.6515 (tt0) cc_final: 0.6287 (tt0) REVERT: D 62 GLN cc_start: 0.6468 (tt0) cc_final: 0.6140 (tt0) REVERT: F 62 GLN cc_start: 0.6465 (tt0) cc_final: 0.6229 (tt0) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 1.5792 time to fit residues: 32.4463 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 : 0.270 ------------------------------------------------------------------------------- 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: 4.9990 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2584 Z= 0.244 Angle : 0.467 4.014 3496 Z= 0.273 Chirality : 0.052 0.128 456 Planarity : 0.002 0.009 428 Dihedral : 5.984 43.072 378 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.10 % Allowed : 11.24 % Favored : 85.66 % 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: -3.40 (0.38), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS F 50 PHE 0.009 0.002 PHE B 94 TYR 0.009 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.282 Fit side-chains REVERT: A 79 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7232 (tt0) REVERT: B 79 GLN cc_start: 0.7900 (pt0) cc_final: 0.7661 (pt0) REVERT: F 79 GLN cc_start: 0.7774 (pt0) cc_final: 0.7265 (tt0) outliers start: 8 outliers final: 0 residues processed: 25 average time/residue: 0.7279 time to fit residues: 19.1628 Evaluate side-chains 17 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 0.0370 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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: 0.7340 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 2584 Z= 0.098 Angle : 0.357 2.721 3496 Z= 0.213 Chirality : 0.051 0.133 456 Planarity : 0.002 0.014 428 Dihedral : 3.430 12.347 378 Min Nonbonded Distance : 2.661 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.55 % Allowed : 13.95 % 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: -2.63 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 50 PHE 0.005 0.001 PHE B 94 TYR 0.005 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.264 Fit side-chains REVERT: A 79 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: F 62 GLN cc_start: 0.6986 (tt0) cc_final: 0.6731 (tm-30) REVERT: F 79 GLN cc_start: 0.7762 (pt0) cc_final: 0.7289 (tt0) outliers start: 4 outliers final: 3 residues processed: 17 average time/residue: 1.0640 time to fit residues: 18.8940 Evaluate side-chains 20 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E 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: 8.9990 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN E 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2584 Z= 0.221 Angle : 0.421 3.300 3496 Z= 0.251 Chirality : 0.050 0.123 456 Planarity : 0.002 0.012 428 Dihedral : 4.081 13.630 378 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.94 % Allowed : 17.05 % Favored : 81.01 % 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: -2.41 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS A 50 PHE 0.008 0.002 PHE B 94 TYR 0.007 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.271 Fit side-chains REVERT: F 62 GLN cc_start: 0.6989 (tt0) cc_final: 0.6745 (tm-30) REVERT: F 79 GLN cc_start: 0.7802 (pt0) cc_final: 0.7347 (tt0) outliers start: 5 outliers final: 4 residues processed: 22 average time/residue: 1.2060 time to fit residues: 27.4061 Evaluate side-chains 21 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E 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: 20.0000 chunk 25 optimal weight: 0.0170 chunk 14 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 31 optimal weight: 0.3980 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 0.3980 chunk 20 optimal weight: 10.0000 overall best weight: 2.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2584 Z= 0.287 Angle : 0.456 3.153 3496 Z= 0.271 Chirality : 0.051 0.119 456 Planarity : 0.003 0.011 428 Dihedral : 4.485 16.557 378 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.71 % Allowed : 20.93 % Favored : 76.36 % 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: -2.40 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.005 HIS A 50 PHE 0.007 0.002 PHE A 94 TYR 0.007 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.286 Fit side-chains REVERT: A 79 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7169 (tt0) REVERT: F 79 GLN cc_start: 0.7813 (pt0) cc_final: 0.7523 (tt0) outliers start: 7 outliers final: 4 residues processed: 22 average time/residue: 1.5274 time to fit residues: 34.5237 Evaluate side-chains 25 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E 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: 4.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 0.0170 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 0.2980 chunk 25 optimal weight: 4.9990 overall best weight: 2.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN E 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2584 Z= 0.233 Angle : 0.416 3.226 3496 Z= 0.249 Chirality : 0.050 0.119 456 Planarity : 0.002 0.010 428 Dihedral : 4.183 15.400 378 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.43 % Allowed : 20.16 % Favored : 74.42 % 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: -2.35 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.005 HIS F 50 PHE 0.006 0.001 PHE A 94 TYR 0.007 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 20 time to evaluate : 0.271 Fit side-chains REVERT: A 79 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7131 (tt0) REVERT: F 62 GLN cc_start: 0.6915 (tt0) cc_final: 0.6637 (tm-30) REVERT: F 79 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7491 (tt0) outliers start: 14 outliers final: 10 residues processed: 25 average time/residue: 1.1676 time to fit residues: 30.1431 Evaluate side-chains 32 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 20 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 79 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 6 optimal weight: 0.0970 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN D 79 GLN E 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 2584 Z= 0.084 Angle : 0.327 2.404 3496 Z= 0.198 Chirality : 0.050 0.122 456 Planarity : 0.001 0.009 428 Dihedral : 3.209 11.566 378 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.88 % Allowed : 20.54 % Favored : 75.58 % 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: -2.07 (0.43), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 50 PHE 0.004 0.001 PHE A 94 TYR 0.005 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 21 time to evaluate : 0.271 Fit side-chains REVERT: A 79 GLN cc_start: 0.7392 (pt0) cc_final: 0.7038 (tt0) REVERT: E 79 GLN cc_start: 0.7637 (pt0) cc_final: 0.7250 (tt0) REVERT: F 62 GLN cc_start: 0.6846 (tt0) cc_final: 0.6576 (tm-30) REVERT: F 79 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7481 (tt0) outliers start: 10 outliers final: 7 residues processed: 26 average time/residue: 1.2905 time to fit residues: 34.5421 Evaluate side-chains 27 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 79 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 32 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN E 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2584 Z= 0.232 Angle : 0.417 4.457 3496 Z= 0.249 Chirality : 0.049 0.120 456 Planarity : 0.002 0.009 428 Dihedral : 3.946 14.022 378 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.43 % Allowed : 20.16 % Favored : 74.42 % 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: -2.14 (0.42), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS F 50 PHE 0.006 0.001 PHE A 94 TYR 0.006 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 20 time to evaluate : 0.275 Fit side-chains REVERT: A 79 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.7140 (tt0) REVERT: F 62 GLN cc_start: 0.6852 (tt0) cc_final: 0.6588 (tm-30) REVERT: F 79 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7458 (tt0) outliers start: 14 outliers final: 11 residues processed: 26 average time/residue: 1.2364 time to fit residues: 33.1535 Evaluate side-chains 33 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 20 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 79 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.1980 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN E 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2584 Z= 0.125 Angle : 0.365 5.862 3496 Z= 0.219 Chirality : 0.050 0.121 456 Planarity : 0.002 0.011 428 Dihedral : 3.480 12.462 378 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.49 % Allowed : 22.09 % Favored : 74.42 % 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: -2.01 (0.43), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS F 50 PHE 0.005 0.001 PHE A 94 TYR 0.005 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.285 Fit side-chains REVERT: A 79 GLN cc_start: 0.7411 (pt0) cc_final: 0.7030 (tt0) REVERT: F 62 GLN cc_start: 0.6886 (tt0) cc_final: 0.6619 (tm-30) REVERT: F 79 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7457 (tt0) outliers start: 9 outliers final: 6 residues processed: 23 average time/residue: 1.4440 time to fit residues: 34.1614 Evaluate side-chains 27 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 79 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN E 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2584 Z= 0.153 Angle : 0.372 4.859 3496 Z= 0.223 Chirality : 0.049 0.119 456 Planarity : 0.002 0.014 428 Dihedral : 3.522 13.621 378 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.26 % Allowed : 21.32 % Favored : 74.42 % 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: -2.01 (0.43), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS F 50 PHE 0.005 0.001 PHE A 94 TYR 0.005 0.001 TYR C 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.267 Fit side-chains REVERT: F 62 GLN cc_start: 0.6870 (tt0) cc_final: 0.6589 (tm-30) REVERT: F 79 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7441 (tt0) outliers start: 11 outliers final: 10 residues processed: 25 average time/residue: 1.2519 time to fit residues: 32.2396 Evaluate side-chains 31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 79 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 20 optimal weight: 0.0870 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN E 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.189957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.152389 restraints weight = 2485.485| |-----------------------------------------------------------------------------| r_work (start): 0.4452 rms_B_bonded: 2.86 r_work: 0.4349 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 2584 Z= 0.320 Angle : 1.970 59.178 3496 Z= 1.185 Chirality : 0.054 0.267 456 Planarity : 0.003 0.029 428 Dihedral : 3.697 16.548 378 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.26 % Allowed : 21.32 % Favored : 74.42 % Cbeta Deviations : 0.64 % 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: -2.04 (0.43), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS F 50 PHE 0.005 0.001 PHE A 94 TYR 0.006 0.001 TYR C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1301.49 seconds wall clock time: 24 minutes 7.70 seconds (1447.70 seconds total)