Starting phenix.real_space_refine on Wed Mar 5 16:00:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ynp_33968/03_2025/7ynp_33968_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ynp_33968/03_2025/7ynp_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_33968/03_2025/7ynp_33968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ynp_33968/03_2025/7ynp_33968.map" model { file = "/net/cci-nas-00/data/ceres_data/7ynp_33968/03_2025/7ynp_33968_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ynp_33968/03_2025/7ynp_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-5624/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: 2.12, per 1000 atoms: 0.83 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: 0.66 Conformation dependent library (CDL) restraints added in 346.2 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: 0.47 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: 0.77 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: 0.02 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' } 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: 1.880 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.680 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.930 ------------------------------------------------------------------------------- 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 : 0.285 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: 1.4745 time to fit residues: 30.3630 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 : 0.251 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.170752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.131523 restraints weight = 2506.023| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 3.04 r_work: 0.4216 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 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 : 0.277 Fit side-chains REVERT: A 54 THR cc_start: 0.7089 (m) cc_final: 0.6837 (p) REVERT: A 62 GLN cc_start: 0.6672 (tt0) cc_final: 0.6298 (tm-30) REVERT: A 79 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7543 (tt0) REVERT: C 62 GLN cc_start: 0.6880 (tt0) cc_final: 0.6481 (tm-30) REVERT: D 62 GLN cc_start: 0.6727 (tt0) cc_final: 0.6439 (tm-30) REVERT: F 79 GLN cc_start: 0.8130 (pt0) cc_final: 0.7614 (tt0) outliers start: 8 outliers final: 0 residues processed: 25 average time/residue: 0.7222 time to fit residues: 19.0409 Evaluate side-chains 18 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 23 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 30 optimal weight: 0.0010 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 overall best weight: 2.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.183106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.144884 restraints weight = 2355.294| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 2.90 r_work: 0.4234 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3655 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 : 0.441 3.356 3496 Z= 0.261 Chirality : 0.051 0.126 456 Planarity : 0.002 0.014 428 Dihedral : 4.342 16.490 378 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.94 % Allowed : 15.89 % Favored : 82.17 % 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: -2.72 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.005 HIS F 50 PHE 0.011 0.002 PHE B 94 TYR 0.007 0.002 TYR A 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 30 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.251 Fit side-chains REVERT: A 62 GLN cc_start: 0.6697 (tt0) cc_final: 0.6246 (tm-30) REVERT: C 62 GLN cc_start: 0.6784 (tt0) cc_final: 0.6388 (tm-30) REVERT: D 62 GLN cc_start: 0.6800 (tt0) cc_final: 0.6455 (tm-30) REVERT: E 62 GLN cc_start: 0.7872 (tt0) cc_final: 0.7555 (tt0) REVERT: F 79 GLN cc_start: 0.8101 (pt0) cc_final: 0.7661 (tt0) outliers start: 5 outliers final: 4 residues processed: 25 average time/residue: 1.2142 time to fit residues: 31.2940 Evaluate side-chains 24 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 54 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.187610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.149660 restraints weight = 2353.363| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 2.79 r_work: 0.4271 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.4126 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2584 Z= 0.221 Angle : 0.414 3.515 3496 Z= 0.247 Chirality : 0.050 0.117 456 Planarity : 0.002 0.013 428 Dihedral : 4.184 15.056 378 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % 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: -2.55 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS D 50 PHE 0.006 0.002 PHE B 94 TYR 0.006 0.001 TYR A 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 29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.259 Fit side-chains REVERT: A 62 GLN cc_start: 0.7030 (tt0) cc_final: 0.6622 (tm-30) REVERT: A 83 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7181 (mt-10) REVERT: B 62 GLN cc_start: 0.7711 (tt0) cc_final: 0.7413 (tm-30) REVERT: C 62 GLN cc_start: 0.6967 (tt0) cc_final: 0.6565 (tm-30) REVERT: D 62 GLN cc_start: 0.6917 (tt0) cc_final: 0.6602 (tm-30) REVERT: E 62 GLN cc_start: 0.7883 (tt0) cc_final: 0.7645 (tt0) REVERT: F 62 GLN cc_start: 0.7249 (tt0) cc_final: 0.6865 (tm-30) REVERT: F 79 GLN cc_start: 0.8160 (pt0) cc_final: 0.7773 (tt0) outliers start: 8 outliers final: 7 residues processed: 22 average time/residue: 1.3378 time to fit residues: 30.3425 Evaluate side-chains 29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 83 GLU 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 54 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 26 optimal weight: 0.0060 chunk 35 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 overall best weight: 2.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN E 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.186849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.149131 restraints weight = 2367.432| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 2.80 r_work: 0.4268 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2584 Z= 0.278 Angle : 0.459 3.693 3496 Z= 0.272 Chirality : 0.050 0.119 456 Planarity : 0.003 0.011 428 Dihedral : 4.619 17.775 378 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.65 % Allowed : 17.83 % Favored : 77.52 % 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: -2.61 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.005 HIS A 50 PHE 0.006 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 38 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.258 Fit side-chains REVERT: A 62 GLN cc_start: 0.6932 (tt0) cc_final: 0.6567 (tm-30) REVERT: A 79 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: B 62 GLN cc_start: 0.7562 (tt0) cc_final: 0.7266 (tm-30) REVERT: C 62 GLN cc_start: 0.6854 (tt0) cc_final: 0.6534 (tm-30) REVERT: D 62 GLN cc_start: 0.6818 (tt0) cc_final: 0.6514 (tm-30) REVERT: E 62 GLN cc_start: 0.7800 (tt0) cc_final: 0.7542 (tt0) REVERT: F 62 GLN cc_start: 0.7106 (tt0) cc_final: 0.6754 (tm-30) REVERT: F 79 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7800 (tt0) outliers start: 12 outliers final: 9 residues processed: 29 average time/residue: 1.1682 time to fit residues: 34.9072 Evaluate side-chains 36 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 79 GLN 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 C residue 79 GLN 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 F residue 54 THR Chi-restraints excluded: chain F residue 79 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 21 optimal weight: 0.0570 chunk 14 optimal weight: 2.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.191771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.154694 restraints weight = 2367.707| |-----------------------------------------------------------------------------| r_work (start): 0.4456 rms_B_bonded: 2.85 r_work: 0.4335 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.011 2584 Z= 0.100 Angle : 0.343 2.807 3496 Z= 0.207 Chirality : 0.051 0.124 456 Planarity : 0.001 0.010 428 Dihedral : 3.505 12.857 378 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.49 % Allowed : 19.77 % Favored : 76.74 % 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: -2.32 (0.42), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS F 50 PHE 0.004 0.001 PHE A 94 TYR 0.005 0.001 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 30 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.254 Fit side-chains REVERT: A 62 GLN cc_start: 0.6870 (tt0) cc_final: 0.6443 (tm-30) REVERT: A 79 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: B 62 GLN cc_start: 0.7588 (tt0) cc_final: 0.7322 (tm-30) REVERT: C 62 GLN cc_start: 0.6783 (tt0) cc_final: 0.6341 (tm-30) REVERT: D 62 GLN cc_start: 0.6733 (tt0) cc_final: 0.6431 (tm-30) REVERT: E 62 GLN cc_start: 0.7736 (tt0) cc_final: 0.7486 (tt0) REVERT: F 62 GLN cc_start: 0.7028 (tt0) cc_final: 0.6233 (tm130) REVERT: F 79 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7715 (tt0) outliers start: 9 outliers final: 6 residues processed: 24 average time/residue: 1.2536 time to fit residues: 31.0473 Evaluate side-chains 29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C 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 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 6 optimal weight: 0.4980 chunk 5 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 0.0040 overall best weight: 1.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.191073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.152580 restraints weight = 2401.345| |-----------------------------------------------------------------------------| r_work (start): 0.4439 rms_B_bonded: 2.88 r_work: 0.4311 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2584 Z= 0.172 Angle : 0.380 3.197 3496 Z= 0.228 Chirality : 0.050 0.122 456 Planarity : 0.002 0.009 428 Dihedral : 3.785 14.970 378 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.49 % Allowed : 20.16 % 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: -2.25 (0.42), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS F 50 PHE 0.005 0.001 PHE A 94 TYR 0.006 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: 9 poor density : 22 time to evaluate : 0.279 Fit side-chains REVERT: A 62 GLN cc_start: 0.6831 (tt0) cc_final: 0.6396 (tm-30) REVERT: A 79 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: B 62 GLN cc_start: 0.7581 (tt0) cc_final: 0.7379 (tm-30) REVERT: C 62 GLN cc_start: 0.6795 (tt0) cc_final: 0.6423 (tm-30) REVERT: D 62 GLN cc_start: 0.6759 (tt0) cc_final: 0.6368 (tm-30) REVERT: E 62 GLN cc_start: 0.7782 (tt0) cc_final: 0.7555 (tt0) REVERT: E 83 GLU cc_start: 0.7682 (tp30) cc_final: 0.7307 (tp30) REVERT: F 62 GLN cc_start: 0.7065 (tt0) cc_final: 0.6727 (tm-30) REVERT: F 79 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7726 (tt0) outliers start: 9 outliers final: 7 residues processed: 25 average time/residue: 1.2633 time to fit residues: 32.5679 Evaluate side-chains 31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 55 VAL Chi-restraints excluded: chain C 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 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 20 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.192516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.154230 restraints weight = 2347.531| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 2.85 r_work: 0.4324 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2584 Z= 0.170 Angle : 0.376 3.135 3496 Z= 0.226 Chirality : 0.050 0.121 456 Planarity : 0.002 0.009 428 Dihedral : 3.740 15.094 378 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.26 % Allowed : 19.38 % 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: -2.17 (0.42), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS F 50 PHE 0.005 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 35 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.259 Fit side-chains REVERT: A 62 GLN cc_start: 0.6881 (tt0) cc_final: 0.6475 (tm-30) REVERT: A 79 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: C 62 GLN cc_start: 0.6806 (tt0) cc_final: 0.6444 (tm-30) REVERT: D 62 GLN cc_start: 0.6753 (tt0) cc_final: 0.6345 (tm-30) REVERT: E 62 GLN cc_start: 0.7759 (tt0) cc_final: 0.7546 (tt0) REVERT: F 62 GLN cc_start: 0.7070 (tt0) cc_final: 0.6726 (tm-30) REVERT: F 79 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7716 (tt0) outliers start: 11 outliers final: 9 residues processed: 28 average time/residue: 1.1388 time to fit residues: 32.9029 Evaluate side-chains 35 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 55 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 54 THR 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 26 optimal weight: 0.0970 chunk 22 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 0.0670 chunk 2 optimal weight: 0.5980 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.181715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.142841 restraints weight = 2544.651| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 2.99 r_work: 0.4276 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.018 2584 Z= 0.083 Angle : 0.335 4.619 3496 Z= 0.202 Chirality : 0.050 0.124 456 Planarity : 0.001 0.009 428 Dihedral : 3.062 10.930 378 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.33 % Allowed : 21.71 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.44), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS F 50 PHE 0.004 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 30 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.248 Fit side-chains REVERT: A 62 GLN cc_start: 0.6821 (tt0) cc_final: 0.6377 (tm-30) REVERT: A 79 GLN cc_start: 0.7921 (pt0) cc_final: 0.7407 (tt0) REVERT: C 60 LYS cc_start: 0.7893 (tttp) cc_final: 0.7525 (tmtt) REVERT: C 62 GLN cc_start: 0.6709 (tt0) cc_final: 0.6299 (tm-30) REVERT: C 83 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7290 (mt-10) REVERT: D 62 GLN cc_start: 0.6636 (tt0) cc_final: 0.6186 (tm-30) REVERT: E 62 GLN cc_start: 0.7716 (tt0) cc_final: 0.7479 (tt0) REVERT: F 62 GLN cc_start: 0.6959 (tt0) cc_final: 0.6058 (tm130) REVERT: F 79 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7755 (tt0) outliers start: 6 outliers final: 4 residues processed: 25 average time/residue: 1.4240 time to fit residues: 36.5336 Evaluate side-chains 29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 92 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 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.191231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.154211 restraints weight = 2431.023| |-----------------------------------------------------------------------------| r_work (start): 0.4464 rms_B_bonded: 2.81 r_work: 0.4359 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.5063 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= 0.182 Angle : 0.393 5.767 3496 Z= 0.235 Chirality : 0.049 0.120 456 Planarity : 0.002 0.011 428 Dihedral : 3.604 14.667 378 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.10 % Allowed : 20.93 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.43), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS A 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: 8 poor density : 24 time to evaluate : 0.258 Fit side-chains REVERT: A 62 GLN cc_start: 0.6868 (tt0) cc_final: 0.6452 (tm-30) REVERT: A 79 GLN cc_start: 0.7957 (pt0) cc_final: 0.7470 (tt0) REVERT: C 62 GLN cc_start: 0.6796 (tt0) cc_final: 0.6444 (tm-30) REVERT: C 83 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7445 (mt-10) REVERT: D 62 GLN cc_start: 0.6661 (tt0) cc_final: 0.6293 (tm-30) REVERT: E 62 GLN cc_start: 0.7734 (tt0) cc_final: 0.7479 (tt0) REVERT: F 62 GLN cc_start: 0.7062 (tt0) cc_final: 0.6696 (tm-30) REVERT: F 79 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7787 (tt0) outliers start: 8 outliers final: 7 residues processed: 26 average time/residue: 1.2462 time to fit residues: 33.3606 Evaluate side-chains 32 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR 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 F residue 79 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.190567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.153279 restraints weight = 2483.330| |-----------------------------------------------------------------------------| r_work (start): 0.4462 rms_B_bonded: 2.88 r_work: 0.4355 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2584 Z= 0.240 Angle : 0.426 5.146 3496 Z= 0.254 Chirality : 0.050 0.120 456 Planarity : 0.002 0.012 428 Dihedral : 3.875 15.763 378 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.65 % Allowed : 19.38 % Favored : 75.97 % 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: -2.05 (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 0.008 0.004 HIS F 50 PHE 0.006 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: 2146.99 seconds wall clock time: 37 minutes 23.84 seconds (2243.84 seconds total)