Starting phenix.real_space_refine on Thu Jun 12 05:17:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hxz_35083/06_2025/8hxz_35083.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hxz_35083/06_2025/8hxz_35083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hxz_35083/06_2025/8hxz_35083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hxz_35083/06_2025/8hxz_35083.map" model { file = "/net/cci-nas-00/data/ceres_data/8hxz_35083/06_2025/8hxz_35083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hxz_35083/06_2025/8hxz_35083.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 328 5.49 5 S 16 5.16 5 C 7628 2.51 5 N 2563 2.21 5 O 3205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13740 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 837 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3345 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "J" Number of atoms: 3379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3379 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "M" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 915 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain breaks: 1 Time building chain proxies: 8.63, per 1000 atoms: 0.63 Number of scatterers: 13740 At special positions: 0 Unit cell: (75.6, 119.7, 142.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 328 15.00 O 3205 8.00 N 2563 7.00 C 7628 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: 3.09 Conformation dependent library (CDL) restraints added in 1.1 seconds 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1644 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 8 sheets defined 66.3% alpha, 6.5% beta 164 base pairs and 294 stacking pairs defined. Time for finding SS restraints: 7.14 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.630A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.571A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.907A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.775A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.090A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.538A pdb=" N GLY B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.292A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.740A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.784A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.959A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 4.272A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.260A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.892A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.884A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.224A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.797A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.065A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.562A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 80 Processing helix chain 'H' and resid 87 through 98 removed outlier: 3.978A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.944A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 89 Processing helix chain 'M' and resid 101 through 131 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.521A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.525A pdb=" N ILE C 78 " --> pdb=" O GLY D 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.999A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'M' and resid 58 through 59 removed outlier: 6.564A pdb=" N PHE M 78 " --> pdb=" O LEU M 28 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 58 through 59 445 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 416 hydrogen bonds 832 hydrogen bond angles 0 basepair planarities 164 basepair parallelities 294 stacking parallelities Total time for adding SS restraints: 6.36 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2322 1.33 - 1.45: 5135 1.45 - 1.58: 6519 1.58 - 1.70: 654 1.70 - 1.82: 30 Bond restraints: 14660 Sorted by residual: bond pdb=" CA ASN G 73 " pdb=" C ASN G 73 " ideal model delta sigma weight residual 1.523 1.571 -0.048 1.41e-02 5.03e+03 1.16e+01 bond pdb=" CA HIS M 18 " pdb=" C HIS M 18 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.34e-02 5.57e+03 1.00e+01 bond pdb=" SG ML3 A 36 " pdb=" CD ML3 A 36 " ideal model delta sigma weight residual 1.815 1.755 0.060 2.00e-02 2.50e+03 8.99e+00 bond pdb=" CB ML3 A 36 " pdb=" SG ML3 A 36 " ideal model delta sigma weight residual 1.817 1.766 0.051 2.00e-02 2.50e+03 6.46e+00 bond pdb=" CA PHE M 17 " pdb=" C PHE M 17 " ideal model delta sigma weight residual 1.527 1.496 0.031 1.35e-02 5.49e+03 5.27e+00 ... (remaining 14655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 20831 2.94 - 5.89: 301 5.89 - 8.83: 53 8.83 - 11.78: 7 11.78 - 14.72: 4 Bond angle restraints: 21196 Sorted by residual: angle pdb=" N HIS M 18 " pdb=" CA HIS M 18 " pdb=" C HIS M 18 " ideal model delta sigma weight residual 110.80 96.08 14.72 2.13e+00 2.20e-01 4.78e+01 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 112.64 120.58 -7.94 1.21e+00 6.83e-01 4.30e+01 angle pdb=" N GLU F 63 " pdb=" CA GLU F 63 " pdb=" CB GLU F 63 " ideal model delta sigma weight residual 110.28 119.35 -9.07 1.55e+00 4.16e-01 3.43e+01 angle pdb=" N VAL D 95 " pdb=" CA VAL D 95 " pdb=" C VAL D 95 " ideal model delta sigma weight residual 110.62 104.73 5.89 1.02e+00 9.61e-01 3.34e+01 angle pdb=" CA ASN G 73 " pdb=" C ASN G 73 " pdb=" N LYS G 74 " ideal model delta sigma weight residual 118.32 110.98 7.34 1.35e+00 5.49e-01 2.95e+01 ... (remaining 21191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 6308 35.86 - 71.73: 1647 71.73 - 107.59: 32 107.59 - 143.45: 1 143.45 - 179.32: 4 Dihedral angle restraints: 7992 sinusoidal: 5444 harmonic: 2548 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 150.91 29.09 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LYS F 79 " pdb=" C LYS F 79 " pdb=" N THR F 80 " pdb=" CA THR F 80 " ideal model delta harmonic sigma weight residual 180.00 151.03 28.97 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA LYS H 31 " pdb=" C LYS H 31 " pdb=" N GLU H 32 " pdb=" CA GLU H 32 " ideal model delta harmonic sigma weight residual -180.00 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 7989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2054 0.067 - 0.134: 287 0.134 - 0.200: 43 0.200 - 0.267: 5 0.267 - 0.334: 2 Chirality restraints: 2391 Sorted by residual: chirality pdb=" CG LEU E 70 " pdb=" CB LEU E 70 " pdb=" CD1 LEU E 70 " pdb=" CD2 LEU E 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB THR D 112 " pdb=" CA THR D 112 " pdb=" OG1 THR D 112 " pdb=" CG2 THR D 112 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 2388 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.055 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO G 80 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.050 5.00e-02 4.00e+02 7.55e-02 9.13e+00 pdb=" N PRO C 80 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 88 " -0.011 2.00e-02 2.50e+03 2.02e-02 8.16e+00 pdb=" CG TYR B 88 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR B 88 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 88 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR B 88 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR B 88 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR B 88 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 88 " -0.006 2.00e-02 2.50e+03 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3364 2.82 - 3.34: 13003 3.34 - 3.86: 29103 3.86 - 4.38: 32268 4.38 - 4.90: 44145 Nonbonded interactions: 121883 Sorted by model distance: nonbonded pdb=" NZ LYS F 79 " pdb=" OP1 DG I 101 " model vdw 2.303 3.120 nonbonded pdb=" N THR H 87 " pdb=" OE2 GLU H 90 " model vdw 2.318 3.120 nonbonded pdb=" O ILE F 50 " pdb=" OG1 THR F 54 " model vdw 2.325 3.040 nonbonded pdb=" NH2 ARG A 42 " pdb=" OP1 DA I 69 " model vdw 2.329 3.120 nonbonded pdb=" NZ LYS G 15 " pdb=" OG SER G 19 " model vdw 2.337 3.120 ... (remaining 121878 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' and resid 37 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = (chain 'H' and resid 28 through 121) } 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=0.00 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: 1.070 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 38.110 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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 : 0.005 0.067 14660 Z= 0.249 Angle : 0.983 14.720 21196 Z= 0.556 Chirality : 0.050 0.334 2391 Planarity : 0.007 0.084 1543 Dihedral : 29.122 179.316 6348 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -1.57 (0.26), residues: 856 helix: -0.86 (0.20), residues: 541 sheet: -0.52 (0.90), residues: 30 loop : -1.15 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 84 HIS 0.014 0.002 HIS B 75 PHE 0.016 0.003 PHE G 25 TYR 0.042 0.004 TYR B 88 ARG 0.012 0.001 ARG H 89 Details of bonding type rmsd hydrogen bonds : bond 0.09779 ( 855) hydrogen bonds : angle 4.87077 ( 2131) covalent geometry : bond 0.00537 (14660) covalent geometry : angle 0.98261 (21196) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8504 (mt-10) REVERT: B 35 ARG cc_start: 0.9274 (mtp-110) cc_final: 0.8911 (mtp-110) REVERT: B 59 LYS cc_start: 0.9445 (tmmt) cc_final: 0.9058 (ttpp) REVERT: B 63 GLU cc_start: 0.8892 (pp20) cc_final: 0.8632 (pp20) REVERT: B 91 LYS cc_start: 0.9644 (tppp) cc_final: 0.9255 (tppp) REVERT: C 36 LYS cc_start: 0.9435 (mmpt) cc_final: 0.9075 (mmmt) REVERT: C 104 GLN cc_start: 0.9084 (mp10) cc_final: 0.8819 (mp10) REVERT: C 111 ILE cc_start: 0.8572 (mm) cc_final: 0.8360 (mm) REVERT: C 112 GLN cc_start: 0.8565 (mp10) cc_final: 0.7286 (mp10) REVERT: D 80 TYR cc_start: 0.8716 (m-80) cc_final: 0.8444 (m-80) REVERT: D 102 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8953 (tp30) REVERT: E 108 ASN cc_start: 0.9229 (t0) cc_final: 0.8490 (t0) REVERT: E 109 LEU cc_start: 0.9619 (mm) cc_final: 0.9137 (mm) REVERT: F 25 ASN cc_start: 0.9414 (m-40) cc_final: 0.9196 (m110) REVERT: F 27 GLN cc_start: 0.9121 (mp10) cc_final: 0.8764 (mp10) REVERT: F 59 LYS cc_start: 0.9376 (ptmm) cc_final: 0.9167 (ptmm) REVERT: F 63 GLU cc_start: 0.9306 (pm20) cc_final: 0.9068 (pm20) REVERT: F 88 TYR cc_start: 0.8692 (m-10) cc_final: 0.7946 (m-10) REVERT: F 93 GLN cc_start: 0.8450 (tm-30) cc_final: 0.7910 (tm-30) REVERT: G 56 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8276 (mm-30) REVERT: G 92 GLU cc_start: 0.8359 (tt0) cc_final: 0.8066 (tt0) REVERT: G 112 GLN cc_start: 0.9081 (mp10) cc_final: 0.8685 (mp10) REVERT: H 65 ASP cc_start: 0.9349 (t0) cc_final: 0.9049 (t0) REVERT: H 92 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8623 (tm-30) REVERT: H 97 LEU cc_start: 0.9180 (tt) cc_final: 0.8896 (tt) REVERT: H 103 LEU cc_start: 0.9451 (mt) cc_final: 0.8816 (mt) REVERT: M 89 ASP cc_start: 0.7249 (m-30) cc_final: 0.7028 (m-30) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.3513 time to fit residues: 122.5103 Evaluate side-chains 189 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 48 optimal weight: 0.0470 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 35 optimal weight: 0.0670 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 overall best weight: 1.4020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.048253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.033168 restraints weight = 99862.850| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 4.22 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14660 Z= 0.177 Angle : 0.699 8.757 21196 Z= 0.401 Chirality : 0.037 0.162 2391 Planarity : 0.005 0.071 1543 Dihedral : 32.172 179.728 4579 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.37 % Allowed : 13.39 % Favored : 85.25 % 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: -0.56 (0.27), residues: 856 helix: -0.00 (0.21), residues: 548 sheet: -0.41 (0.97), residues: 29 loop : -0.86 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 31 HIS 0.009 0.001 HIS F 75 PHE 0.021 0.002 PHE A 84 TYR 0.042 0.002 TYR B 88 ARG 0.008 0.000 ARG D 26 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 855) hydrogen bonds : angle 3.75530 ( 2131) covalent geometry : bond 0.00384 (14660) covalent geometry : angle 0.69886 (21196) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 212 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9576 (t0) cc_final: 0.9075 (t0) REVERT: B 59 LYS cc_start: 0.9474 (tmmt) cc_final: 0.9067 (ttpp) REVERT: B 63 GLU cc_start: 0.9098 (pp20) cc_final: 0.8841 (pp20) REVERT: B 91 LYS cc_start: 0.9613 (tppp) cc_final: 0.9200 (tppp) REVERT: C 25 PHE cc_start: 0.8823 (m-10) cc_final: 0.8555 (m-10) REVERT: C 36 LYS cc_start: 0.9604 (mmpt) cc_final: 0.9229 (mtmm) REVERT: C 89 ASN cc_start: 0.9790 (m-40) cc_final: 0.9523 (m110) REVERT: C 104 GLN cc_start: 0.9186 (mp10) cc_final: 0.8780 (mp10) REVERT: C 111 ILE cc_start: 0.8606 (mm) cc_final: 0.8379 (mm) REVERT: C 112 GLN cc_start: 0.7858 (mp10) cc_final: 0.7480 (mp10) REVERT: D 34 TYR cc_start: 0.9164 (m-80) cc_final: 0.8955 (m-80) REVERT: D 56 MET cc_start: 0.9443 (tpp) cc_final: 0.9205 (tpp) REVERT: D 80 TYR cc_start: 0.8783 (m-80) cc_final: 0.8075 (m-80) REVERT: D 102 GLU cc_start: 0.9481 (mm-30) cc_final: 0.9278 (mp0) REVERT: D 113 LYS cc_start: 0.9264 (pptt) cc_final: 0.9056 (pptt) REVERT: E 97 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8603 (mt-10) REVERT: E 108 ASN cc_start: 0.9258 (t0) cc_final: 0.8754 (t0) REVERT: F 27 GLN cc_start: 0.9145 (mp10) cc_final: 0.8748 (mp10) REVERT: F 79 LYS cc_start: 0.8840 (pttm) cc_final: 0.8590 (pttm) REVERT: F 88 TYR cc_start: 0.8829 (m-10) cc_final: 0.8568 (m-10) REVERT: G 56 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8334 (mm-30) REVERT: G 61 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8640 (mm-30) REVERT: G 94 ASN cc_start: 0.9075 (m-40) cc_final: 0.8441 (m110) REVERT: G 112 GLN cc_start: 0.8975 (mp10) cc_final: 0.8425 (mp10) REVERT: H 59 MET cc_start: 0.9550 (mmp) cc_final: 0.9347 (mmm) REVERT: H 65 ASP cc_start: 0.9593 (t0) cc_final: 0.9278 (t0) REVERT: H 80 TYR cc_start: 0.8874 (m-80) cc_final: 0.8470 (m-80) REVERT: H 92 GLN cc_start: 0.9254 (tm130) cc_final: 0.8891 (tm-30) REVERT: H 96 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8405 (ptp-110) outliers start: 10 outliers final: 4 residues processed: 212 average time/residue: 0.3265 time to fit residues: 94.3027 Evaluate side-chains 183 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 178 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 96 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 8.9990 chunk 109 optimal weight: 30.0000 chunk 27 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.044856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.030595 restraints weight = 103155.601| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 4.08 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14660 Z= 0.258 Angle : 0.716 8.983 21196 Z= 0.414 Chirality : 0.039 0.174 2391 Planarity : 0.005 0.062 1543 Dihedral : 32.196 178.896 4579 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.19 % Allowed : 16.26 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.27), residues: 856 helix: 0.31 (0.21), residues: 561 sheet: -1.04 (1.40), residues: 15 loop : -0.65 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 31 HIS 0.009 0.002 HIS F 75 PHE 0.016 0.002 PHE D 62 TYR 0.059 0.003 TYR B 88 ARG 0.006 0.001 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.05718 ( 855) hydrogen bonds : angle 3.74180 ( 2131) covalent geometry : bond 0.00566 (14660) covalent geometry : angle 0.71603 (21196) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9527 (t80) cc_final: 0.9121 (t80) REVERT: A 108 ASN cc_start: 0.9579 (t0) cc_final: 0.9153 (t0) REVERT: A 120 MET cc_start: 0.8776 (mmm) cc_final: 0.8130 (mmm) REVERT: B 59 LYS cc_start: 0.9518 (tmmt) cc_final: 0.9124 (ttpp) REVERT: B 63 GLU cc_start: 0.9171 (pp20) cc_final: 0.8957 (pp20) REVERT: B 85 ASP cc_start: 0.8914 (m-30) cc_final: 0.8701 (m-30) REVERT: B 91 LYS cc_start: 0.9668 (tppp) cc_final: 0.9214 (tppp) REVERT: C 36 LYS cc_start: 0.9660 (mmpt) cc_final: 0.9378 (mtmm) REVERT: C 89 ASN cc_start: 0.9821 (m-40) cc_final: 0.9467 (m110) REVERT: C 104 GLN cc_start: 0.9271 (mp10) cc_final: 0.8877 (mp10) REVERT: F 27 GLN cc_start: 0.9065 (mp10) cc_final: 0.8810 (mp10) REVERT: F 91 LYS cc_start: 0.9717 (tppt) cc_final: 0.9439 (ttpp) REVERT: G 61 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8755 (mm-30) REVERT: G 94 ASN cc_start: 0.8931 (m-40) cc_final: 0.8245 (m110) REVERT: G 112 GLN cc_start: 0.8848 (mp10) cc_final: 0.8259 (mp10) REVERT: H 56 MET cc_start: 0.9394 (tpt) cc_final: 0.9179 (tpt) REVERT: H 65 ASP cc_start: 0.9637 (t0) cc_final: 0.9315 (t0) REVERT: H 92 GLN cc_start: 0.9355 (tm130) cc_final: 0.9087 (tm-30) outliers start: 16 outliers final: 8 residues processed: 211 average time/residue: 0.3381 time to fit residues: 95.5579 Evaluate side-chains 187 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 179 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 53 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.043735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.029215 restraints weight = 102656.707| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.68 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14660 Z= 0.284 Angle : 0.742 9.543 21196 Z= 0.424 Chirality : 0.039 0.186 2391 Planarity : 0.005 0.057 1543 Dihedral : 32.237 179.087 4579 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.28 % Allowed : 18.17 % Favored : 78.55 % 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: -0.05 (0.27), residues: 856 helix: 0.40 (0.21), residues: 561 sheet: -1.57 (1.37), residues: 15 loop : -0.61 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 84 HIS 0.009 0.002 HIS M 18 PHE 0.016 0.002 PHE D 62 TYR 0.062 0.003 TYR B 88 ARG 0.005 0.001 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.06022 ( 855) hydrogen bonds : angle 3.76697 ( 2131) covalent geometry : bond 0.00621 (14660) covalent geometry : angle 0.74191 (21196) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9605 (t0) cc_final: 0.9058 (t0) REVERT: A 120 MET cc_start: 0.8818 (mmm) cc_final: 0.8611 (mmm) REVERT: B 59 LYS cc_start: 0.9540 (tmmt) cc_final: 0.9192 (ttpp) REVERT: C 104 GLN cc_start: 0.9086 (mp10) cc_final: 0.8737 (mp10) REVERT: C 112 GLN cc_start: 0.8178 (mp10) cc_final: 0.7477 (mp10) REVERT: D 56 MET cc_start: 0.9357 (tpp) cc_final: 0.9133 (tpp) REVERT: E 84 PHE cc_start: 0.9184 (m-80) cc_final: 0.8889 (m-80) REVERT: E 108 ASN cc_start: 0.9505 (t0) cc_final: 0.8712 (t0) REVERT: E 112 ILE cc_start: 0.9383 (mt) cc_final: 0.8951 (mt) REVERT: F 27 GLN cc_start: 0.9013 (mp10) cc_final: 0.8742 (mp10) REVERT: G 38 ASN cc_start: 0.8572 (t0) cc_final: 0.8351 (t0) REVERT: G 56 GLU cc_start: 0.9303 (OUTLIER) cc_final: 0.8872 (mt-10) REVERT: G 61 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8812 (mm-30) REVERT: G 64 GLU cc_start: 0.9134 (pp20) cc_final: 0.8874 (pp20) REVERT: G 89 ASN cc_start: 0.9508 (m-40) cc_final: 0.9044 (p0) REVERT: G 112 GLN cc_start: 0.8911 (mp10) cc_final: 0.8317 (mp10) REVERT: H 56 MET cc_start: 0.9404 (tpt) cc_final: 0.9112 (tpt) REVERT: H 65 ASP cc_start: 0.9550 (t0) cc_final: 0.9277 (t0) REVERT: H 68 GLU cc_start: 0.9426 (tm-30) cc_final: 0.9208 (tm-30) REVERT: H 92 GLN cc_start: 0.9421 (OUTLIER) cc_final: 0.9172 (tm-30) outliers start: 24 outliers final: 12 residues processed: 219 average time/residue: 0.3177 time to fit residues: 94.4740 Evaluate side-chains 190 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 92 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 109 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 108 optimal weight: 40.0000 chunk 83 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN H 106 HIS ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.043944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.029428 restraints weight = 102782.646| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.80 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14660 Z= 0.253 Angle : 0.735 14.356 21196 Z= 0.420 Chirality : 0.039 0.185 2391 Planarity : 0.005 0.055 1543 Dihedral : 32.159 179.759 4579 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.87 % Allowed : 22.40 % Favored : 74.73 % 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: -0.02 (0.27), residues: 856 helix: 0.43 (0.21), residues: 556 sheet: -1.58 (1.39), residues: 15 loop : -0.59 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 88 HIS 0.004 0.001 HIS D 106 PHE 0.010 0.001 PHE D 62 TYR 0.062 0.002 TYR B 88 ARG 0.005 0.001 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.05402 ( 855) hydrogen bonds : angle 3.68311 ( 2131) covalent geometry : bond 0.00558 (14660) covalent geometry : angle 0.73451 (21196) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9464 (t80) cc_final: 0.9184 (t80) REVERT: A 108 ASN cc_start: 0.9579 (t0) cc_final: 0.9029 (t0) REVERT: B 59 LYS cc_start: 0.9550 (tmmt) cc_final: 0.9274 (ttpp) REVERT: C 104 GLN cc_start: 0.9012 (mp10) cc_final: 0.8657 (mp10) REVERT: C 112 GLN cc_start: 0.7979 (mp10) cc_final: 0.7371 (mp10) REVERT: D 56 MET cc_start: 0.9455 (tpp) cc_final: 0.9239 (tpp) REVERT: D 76 ARG cc_start: 0.9411 (mtm-85) cc_final: 0.9011 (mtm-85) REVERT: E 84 PHE cc_start: 0.9205 (m-80) cc_final: 0.8942 (m-80) REVERT: E 105 GLU cc_start: 0.9282 (tp30) cc_final: 0.9021 (tp30) REVERT: E 108 ASN cc_start: 0.9522 (t0) cc_final: 0.8898 (t0) REVERT: E 112 ILE cc_start: 0.9384 (mt) cc_final: 0.9114 (mt) REVERT: F 27 GLN cc_start: 0.9044 (mp10) cc_final: 0.8756 (mp10) REVERT: F 79 LYS cc_start: 0.9061 (pttm) cc_final: 0.8631 (pttm) REVERT: G 38 ASN cc_start: 0.8598 (t0) cc_final: 0.8284 (t0) REVERT: G 56 GLU cc_start: 0.9260 (OUTLIER) cc_final: 0.8826 (mt-10) REVERT: G 61 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8814 (mm-30) REVERT: G 64 GLU cc_start: 0.9198 (pp20) cc_final: 0.8952 (pp20) REVERT: G 72 ASP cc_start: 0.9272 (m-30) cc_final: 0.9069 (m-30) REVERT: G 112 GLN cc_start: 0.8847 (mp10) cc_final: 0.8251 (mp10) REVERT: H 56 MET cc_start: 0.9439 (tpp) cc_final: 0.9078 (tpt) REVERT: H 76 ARG cc_start: 0.9480 (ttm110) cc_final: 0.9133 (ttp-110) REVERT: H 82 LYS cc_start: 0.9603 (mmmt) cc_final: 0.9364 (mmmt) REVERT: H 92 GLN cc_start: 0.9461 (tm-30) cc_final: 0.9091 (tm-30) REVERT: H 105 LYS cc_start: 0.9497 (ptpp) cc_final: 0.9277 (ptpp) outliers start: 21 outliers final: 14 residues processed: 214 average time/residue: 0.3332 time to fit residues: 96.1438 Evaluate side-chains 196 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 89 ASN ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.046439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.031603 restraints weight = 99907.520| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.84 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14660 Z= 0.172 Angle : 0.722 11.245 21196 Z= 0.407 Chirality : 0.037 0.188 2391 Planarity : 0.005 0.057 1543 Dihedral : 31.799 179.391 4579 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.01 % Allowed : 23.91 % Favored : 73.09 % 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: 0.05 (0.28), residues: 856 helix: 0.43 (0.21), residues: 561 sheet: -1.52 (1.40), residues: 15 loop : -0.45 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 31 HIS 0.003 0.001 HIS E 39 PHE 0.010 0.001 PHE H 62 TYR 0.036 0.002 TYR H 80 ARG 0.006 0.001 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 855) hydrogen bonds : angle 3.55442 ( 2131) covalent geometry : bond 0.00379 (14660) covalent geometry : angle 0.72220 (21196) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9445 (tt0) cc_final: 0.9104 (tp-100) REVERT: A 108 ASN cc_start: 0.9573 (t0) cc_final: 0.8932 (t0) REVERT: A 115 LYS cc_start: 0.9474 (mmmm) cc_final: 0.9164 (mmmt) REVERT: B 59 LYS cc_start: 0.9534 (tmmt) cc_final: 0.9332 (ttpp) REVERT: C 89 ASN cc_start: 0.9767 (m-40) cc_final: 0.9398 (m110) REVERT: C 104 GLN cc_start: 0.8945 (mp10) cc_final: 0.8601 (mp10) REVERT: C 112 GLN cc_start: 0.7899 (mp10) cc_final: 0.7164 (mp10) REVERT: E 50 GLU cc_start: 0.9659 (OUTLIER) cc_final: 0.9407 (pp20) REVERT: E 68 GLN cc_start: 0.9228 (tm-30) cc_final: 0.8972 (tm-30) REVERT: E 84 PHE cc_start: 0.9091 (m-80) cc_final: 0.8817 (m-80) REVERT: E 105 GLU cc_start: 0.9298 (tp30) cc_final: 0.8998 (tp30) REVERT: E 108 ASN cc_start: 0.9504 (t0) cc_final: 0.8816 (t0) REVERT: E 112 ILE cc_start: 0.9412 (mt) cc_final: 0.9185 (mt) REVERT: F 27 GLN cc_start: 0.9004 (mp10) cc_final: 0.8684 (mp10) REVERT: F 79 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8528 (ptpp) REVERT: F 84 MET cc_start: 0.8954 (tpp) cc_final: 0.8734 (tpp) REVERT: F 88 TYR cc_start: 0.8909 (m-10) cc_final: 0.8296 (m-80) REVERT: G 38 ASN cc_start: 0.8186 (t0) cc_final: 0.7829 (t0) REVERT: G 56 GLU cc_start: 0.9221 (OUTLIER) cc_final: 0.8782 (mt-10) REVERT: G 61 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8757 (mm-30) REVERT: G 64 GLU cc_start: 0.9179 (pp20) cc_final: 0.8920 (pp20) REVERT: G 90 ASP cc_start: 0.9406 (t70) cc_final: 0.9168 (t0) REVERT: G 92 GLU cc_start: 0.8462 (tt0) cc_final: 0.7998 (tt0) REVERT: G 94 ASN cc_start: 0.8928 (m-40) cc_final: 0.8066 (m110) REVERT: G 112 GLN cc_start: 0.8825 (mp10) cc_final: 0.8140 (mp10) REVERT: H 76 ARG cc_start: 0.9459 (ttm110) cc_final: 0.9073 (ttp-110) REVERT: H 92 GLN cc_start: 0.9474 (tm-30) cc_final: 0.9147 (tm-30) outliers start: 22 outliers final: 13 residues processed: 225 average time/residue: 0.3480 time to fit residues: 105.4230 Evaluate side-chains 214 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 31 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 46 optimal weight: 0.0060 chunk 113 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 41 optimal weight: 0.0770 chunk 54 optimal weight: 0.3980 chunk 25 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.8958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.045777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.031130 restraints weight = 103680.597| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.83 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14660 Z= 0.189 Angle : 0.739 14.314 21196 Z= 0.413 Chirality : 0.037 0.192 2391 Planarity : 0.005 0.057 1543 Dihedral : 31.750 177.822 4579 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.28 % Allowed : 25.27 % Favored : 71.45 % 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: 0.18 (0.28), residues: 856 helix: 0.56 (0.21), residues: 556 sheet: -1.44 (1.45), residues: 15 loop : -0.47 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 31 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE D 62 TYR 0.030 0.002 TYR H 80 ARG 0.008 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 855) hydrogen bonds : angle 3.55291 ( 2131) covalent geometry : bond 0.00420 (14660) covalent geometry : angle 0.73923 (21196) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9379 (tt0) cc_final: 0.9038 (tp-100) REVERT: A 108 ASN cc_start: 0.9543 (t0) cc_final: 0.8848 (t0) REVERT: A 115 LYS cc_start: 0.9519 (mmmm) cc_final: 0.9216 (mmmt) REVERT: A 125 GLN cc_start: 0.9255 (mt0) cc_final: 0.8829 (mt0) REVERT: B 84 MET cc_start: 0.9133 (tpp) cc_final: 0.8557 (tpp) REVERT: B 88 TYR cc_start: 0.9158 (m-80) cc_final: 0.8133 (m-80) REVERT: C 104 GLN cc_start: 0.8890 (mp10) cc_final: 0.8496 (mp10) REVERT: C 112 GLN cc_start: 0.7878 (mp10) cc_final: 0.7281 (mp10) REVERT: D 31 LYS cc_start: 0.8858 (mmtt) cc_final: 0.8647 (mmtm) REVERT: D 73 GLU cc_start: 0.8874 (tp30) cc_final: 0.8667 (tp30) REVERT: D 102 GLU cc_start: 0.8778 (tp30) cc_final: 0.8553 (tp30) REVERT: E 50 GLU cc_start: 0.9654 (OUTLIER) cc_final: 0.9352 (pp20) REVERT: E 64 LYS cc_start: 0.9512 (mmtm) cc_final: 0.9044 (mmtm) REVERT: E 68 GLN cc_start: 0.9216 (tm-30) cc_final: 0.8957 (tm-30) REVERT: E 84 PHE cc_start: 0.9062 (m-80) cc_final: 0.8807 (m-80) REVERT: E 97 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8233 (mt-10) REVERT: E 105 GLU cc_start: 0.9301 (tp30) cc_final: 0.9023 (tp30) REVERT: E 108 ASN cc_start: 0.9410 (t0) cc_final: 0.8678 (t0) REVERT: E 112 ILE cc_start: 0.9406 (mt) cc_final: 0.9111 (mt) REVERT: F 27 GLN cc_start: 0.8966 (mp10) cc_final: 0.8705 (mp10) REVERT: F 31 LYS cc_start: 0.9607 (tmtt) cc_final: 0.9350 (tptp) REVERT: F 79 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8515 (ptpp) REVERT: F 88 TYR cc_start: 0.8909 (m-10) cc_final: 0.8577 (m-80) REVERT: G 38 ASN cc_start: 0.8245 (t0) cc_final: 0.7839 (t0) REVERT: G 56 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8760 (mt-10) REVERT: G 61 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8760 (mm-30) REVERT: G 64 GLU cc_start: 0.9172 (pp20) cc_final: 0.8922 (pp20) REVERT: G 72 ASP cc_start: 0.9075 (m-30) cc_final: 0.8721 (p0) REVERT: G 92 GLU cc_start: 0.8467 (tt0) cc_final: 0.8054 (tt0) REVERT: G 94 ASN cc_start: 0.8844 (m-40) cc_final: 0.7986 (m110) REVERT: G 112 GLN cc_start: 0.8780 (mp10) cc_final: 0.8117 (mp10) REVERT: H 56 MET cc_start: 0.9359 (tpt) cc_final: 0.9128 (tpt) REVERT: H 76 ARG cc_start: 0.9467 (ttm110) cc_final: 0.9159 (ttp-110) REVERT: H 92 GLN cc_start: 0.9508 (tm-30) cc_final: 0.9166 (tm-30) outliers start: 24 outliers final: 14 residues processed: 216 average time/residue: 0.3461 time to fit residues: 100.6618 Evaluate side-chains 217 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 79 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** 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 = 0.3356 r_free = 0.3356 target = 0.046040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.031373 restraints weight = 99467.951| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.83 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14660 Z= 0.192 Angle : 0.758 12.955 21196 Z= 0.421 Chirality : 0.038 0.194 2391 Planarity : 0.005 0.068 1543 Dihedral : 31.713 178.027 4579 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.01 % Allowed : 25.55 % Favored : 71.45 % 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: 0.23 (0.28), residues: 856 helix: 0.60 (0.21), residues: 558 sheet: -1.57 (1.44), residues: 15 loop : -0.44 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 88 HIS 0.005 0.001 HIS F 75 PHE 0.007 0.001 PHE H 62 TYR 0.032 0.002 TYR H 80 ARG 0.008 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 855) hydrogen bonds : angle 3.55413 ( 2131) covalent geometry : bond 0.00428 (14660) covalent geometry : angle 0.75784 (21196) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 209 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9056 (tp) cc_final: 0.8782 (tp) REVERT: A 61 LEU cc_start: 0.9116 (mp) cc_final: 0.8749 (mp) REVERT: A 67 PHE cc_start: 0.9434 (t80) cc_final: 0.9069 (t80) REVERT: A 108 ASN cc_start: 0.9523 (t0) cc_final: 0.8968 (t0) REVERT: A 115 LYS cc_start: 0.9545 (mmmm) cc_final: 0.9228 (mmmt) REVERT: C 25 PHE cc_start: 0.9110 (m-10) cc_final: 0.8685 (m-10) REVERT: C 104 GLN cc_start: 0.9014 (mp10) cc_final: 0.8607 (mp10) REVERT: C 112 GLN cc_start: 0.7705 (mp10) cc_final: 0.7060 (mp10) REVERT: D 31 LYS cc_start: 0.8955 (mmtt) cc_final: 0.8717 (mmtm) REVERT: D 102 GLU cc_start: 0.8989 (tp30) cc_final: 0.8644 (tp30) REVERT: E 50 GLU cc_start: 0.9675 (OUTLIER) cc_final: 0.9369 (pp20) REVERT: E 64 LYS cc_start: 0.9504 (mmtm) cc_final: 0.9056 (mmtm) REVERT: E 68 GLN cc_start: 0.9253 (tm-30) cc_final: 0.9004 (tm-30) REVERT: E 84 PHE cc_start: 0.9205 (m-80) cc_final: 0.8929 (m-80) REVERT: E 97 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8321 (mt-10) REVERT: E 105 GLU cc_start: 0.9328 (tp30) cc_final: 0.9033 (tp30) REVERT: E 108 ASN cc_start: 0.9331 (t0) cc_final: 0.8659 (t0) REVERT: E 112 ILE cc_start: 0.9326 (mt) cc_final: 0.9018 (mt) REVERT: F 27 GLN cc_start: 0.9055 (mp10) cc_final: 0.8769 (mp10) REVERT: F 79 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8661 (ptpp) REVERT: G 38 ASN cc_start: 0.8224 (t0) cc_final: 0.7786 (t0) REVERT: G 56 GLU cc_start: 0.9276 (OUTLIER) cc_final: 0.8828 (mt-10) REVERT: G 61 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8896 (mm-30) REVERT: G 64 GLU cc_start: 0.9317 (pp20) cc_final: 0.9075 (pp20) REVERT: G 72 ASP cc_start: 0.9132 (m-30) cc_final: 0.8804 (p0) REVERT: G 92 GLU cc_start: 0.8525 (tt0) cc_final: 0.8119 (tt0) REVERT: G 94 ASN cc_start: 0.8872 (m-40) cc_final: 0.8090 (m110) REVERT: G 112 GLN cc_start: 0.8659 (mp10) cc_final: 0.8060 (mp10) REVERT: H 56 MET cc_start: 0.9506 (tpt) cc_final: 0.9290 (tpt) REVERT: H 76 ARG cc_start: 0.9510 (ttm110) cc_final: 0.9226 (ttp-110) REVERT: H 92 GLN cc_start: 0.9515 (tm-30) cc_final: 0.9201 (tm-30) outliers start: 22 outliers final: 15 residues processed: 219 average time/residue: 0.3151 time to fit residues: 93.9900 Evaluate side-chains 219 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 79 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 20.0000 chunk 52 optimal weight: 0.6980 chunk 101 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** 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 = 0.3288 r_free = 0.3288 target = 0.042983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.028651 restraints weight = 103314.322| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.55 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 14660 Z= 0.306 Angle : 0.826 16.108 21196 Z= 0.459 Chirality : 0.041 0.212 2391 Planarity : 0.006 0.057 1543 Dihedral : 32.144 178.368 4579 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 22.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.87 % Allowed : 27.46 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.27), residues: 856 helix: 0.37 (0.21), residues: 563 sheet: -1.67 (1.42), residues: 15 loop : -0.57 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 88 HIS 0.009 0.002 HIS M 80 PHE 0.013 0.002 PHE D 62 TYR 0.075 0.003 TYR F 88 ARG 0.008 0.001 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.06743 ( 855) hydrogen bonds : angle 3.83622 ( 2131) covalent geometry : bond 0.00677 (14660) covalent geometry : angle 0.82613 (21196) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9552 (t0) cc_final: 0.8939 (t0) REVERT: A 115 LYS cc_start: 0.9545 (mmmm) cc_final: 0.9242 (mmmt) REVERT: A 125 GLN cc_start: 0.9206 (mt0) cc_final: 0.8855 (mt0) REVERT: C 39 TYR cc_start: 0.9087 (m-80) cc_final: 0.8850 (m-80) REVERT: C 104 GLN cc_start: 0.8955 (mp10) cc_final: 0.8551 (mp10) REVERT: C 112 GLN cc_start: 0.7895 (mp10) cc_final: 0.7338 (mp10) REVERT: D 31 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8684 (mmtm) REVERT: D 102 GLU cc_start: 0.8856 (tp30) cc_final: 0.8594 (tp30) REVERT: D 105 LYS cc_start: 0.9349 (mmtt) cc_final: 0.9102 (ptpp) REVERT: E 50 GLU cc_start: 0.9692 (OUTLIER) cc_final: 0.9341 (pp20) REVERT: E 84 PHE cc_start: 0.9266 (m-80) cc_final: 0.9045 (m-80) REVERT: E 105 GLU cc_start: 0.9353 (tp30) cc_final: 0.9043 (tp30) REVERT: E 108 ASN cc_start: 0.9437 (t0) cc_final: 0.8632 (t0) REVERT: E 112 ILE cc_start: 0.9387 (mt) cc_final: 0.9104 (mt) REVERT: F 79 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8853 (ptpp) REVERT: F 84 MET cc_start: 0.8984 (tpp) cc_final: 0.8553 (tpp) REVERT: F 88 TYR cc_start: 0.9088 (m-10) cc_final: 0.8634 (m-80) REVERT: G 38 ASN cc_start: 0.8202 (t0) cc_final: 0.7872 (t0) REVERT: G 56 GLU cc_start: 0.9254 (OUTLIER) cc_final: 0.8809 (mt-10) REVERT: G 61 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8955 (mm-30) REVERT: G 64 GLU cc_start: 0.9336 (pp20) cc_final: 0.9100 (pp20) REVERT: G 72 ASP cc_start: 0.9176 (m-30) cc_final: 0.8840 (p0) REVERT: G 112 GLN cc_start: 0.8795 (mp10) cc_final: 0.8158 (mp10) REVERT: H 56 MET cc_start: 0.9445 (tpt) cc_final: 0.9244 (tpt) REVERT: H 92 GLN cc_start: 0.9541 (tm-30) cc_final: 0.9262 (tm-30) outliers start: 21 outliers final: 15 residues processed: 210 average time/residue: 0.3210 time to fit residues: 91.3649 Evaluate side-chains 205 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain M residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** 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 = 0.3284 r_free = 0.3284 target = 0.042979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.028602 restraints weight = 104295.608| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.64 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.5197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 14660 Z= 0.295 Angle : 0.840 16.752 21196 Z= 0.465 Chirality : 0.041 0.202 2391 Planarity : 0.006 0.077 1543 Dihedral : 32.199 179.006 4579 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.60 % Allowed : 28.28 % Favored : 69.13 % 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: -0.15 (0.28), residues: 856 helix: 0.34 (0.21), residues: 561 sheet: -0.39 (1.16), residues: 25 loop : -0.79 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 88 HIS 0.005 0.002 HIS B 75 PHE 0.011 0.002 PHE A 104 TYR 0.078 0.003 TYR F 88 ARG 0.008 0.001 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.06076 ( 855) hydrogen bonds : angle 3.82286 ( 2131) covalent geometry : bond 0.00654 (14660) covalent geometry : angle 0.83991 (21196) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 198 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9557 (t0) cc_final: 0.8942 (t0) REVERT: A 115 LYS cc_start: 0.9573 (mmmm) cc_final: 0.9254 (mmmt) REVERT: A 125 GLN cc_start: 0.9226 (mt0) cc_final: 0.8818 (mt0) REVERT: C 39 TYR cc_start: 0.9010 (m-80) cc_final: 0.8747 (m-80) REVERT: C 104 GLN cc_start: 0.8948 (mp10) cc_final: 0.8581 (mp10) REVERT: C 112 GLN cc_start: 0.7855 (mp10) cc_final: 0.7271 (mp10) REVERT: D 102 GLU cc_start: 0.8893 (tp30) cc_final: 0.8690 (tp30) REVERT: E 50 GLU cc_start: 0.9685 (OUTLIER) cc_final: 0.9356 (pp20) REVERT: E 76 GLN cc_start: 0.9310 (tp-100) cc_final: 0.9057 (tp-100) REVERT: E 84 PHE cc_start: 0.9250 (m-80) cc_final: 0.9043 (m-80) REVERT: E 97 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8127 (mt-10) REVERT: E 105 GLU cc_start: 0.9340 (tp30) cc_final: 0.9032 (tp30) REVERT: E 108 ASN cc_start: 0.9419 (t0) cc_final: 0.8615 (t0) REVERT: E 112 ILE cc_start: 0.9337 (mt) cc_final: 0.9037 (mt) REVERT: F 27 GLN cc_start: 0.9068 (mp10) cc_final: 0.8825 (mp10) REVERT: F 79 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8839 (ptpp) REVERT: F 84 MET cc_start: 0.8994 (tpp) cc_final: 0.8556 (tpp) REVERT: F 88 TYR cc_start: 0.9073 (m-10) cc_final: 0.8562 (m-80) REVERT: G 38 ASN cc_start: 0.8107 (t0) cc_final: 0.7737 (t0) REVERT: G 56 GLU cc_start: 0.9274 (OUTLIER) cc_final: 0.8849 (mt-10) REVERT: G 61 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8900 (mm-30) REVERT: G 64 GLU cc_start: 0.9380 (pp20) cc_final: 0.9172 (pp20) REVERT: G 72 ASP cc_start: 0.9221 (m-30) cc_final: 0.8867 (p0) REVERT: G 112 GLN cc_start: 0.8832 (mp10) cc_final: 0.8236 (mp10) REVERT: H 56 MET cc_start: 0.9455 (tpt) cc_final: 0.9017 (tpp) REVERT: H 76 ARG cc_start: 0.9367 (ttm110) cc_final: 0.9059 (ttp-110) REVERT: H 92 GLN cc_start: 0.9532 (tm-30) cc_final: 0.9209 (tm-30) outliers start: 19 outliers final: 14 residues processed: 209 average time/residue: 0.3099 time to fit residues: 88.6836 Evaluate side-chains 205 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain M residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 chunk 3 optimal weight: 0.0770 chunk 9 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** 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 = 0.3327 r_free = 0.3327 target = 0.044826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.029875 restraints weight = 103082.854| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.72 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14660 Z= 0.208 Angle : 0.831 17.808 21196 Z= 0.455 Chirality : 0.039 0.206 2391 Planarity : 0.005 0.062 1543 Dihedral : 31.983 178.933 4579 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.60 % Allowed : 29.10 % Favored : 68.31 % 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: -0.05 (0.28), residues: 856 helix: 0.41 (0.21), residues: 556 sheet: -1.70 (1.43), residues: 15 loop : -0.62 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 88 HIS 0.004 0.001 HIS F 75 PHE 0.008 0.001 PHE H 62 TYR 0.065 0.003 TYR F 88 ARG 0.008 0.001 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 855) hydrogen bonds : angle 3.73947 ( 2131) covalent geometry : bond 0.00467 (14660) covalent geometry : angle 0.83083 (21196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6005.02 seconds wall clock time: 104 minutes 2.19 seconds (6242.19 seconds total)