Starting phenix.real_space_refine on Sun Nov 17 11:17:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxz_35083/11_2024/8hxz_35083.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxz_35083/11_2024/8hxz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxz_35083/11_2024/8hxz_35083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxz_35083/11_2024/8hxz_35083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxz_35083/11_2024/8hxz_35083.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxz_35083/11_2024/8hxz_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 8.86, per 1000 atoms: 0.64 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: 3.53 Conformation dependent library (CDL) restraints added in 1.0 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: 7.30 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: 6.01 Time building geometry restraints manager: 4.11 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: 0.810 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: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 39.490 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.390 ------------------------------------------------------------------------------- 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= 0.311 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 *********************** 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 : 1.051 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: 0.3640 time to fit residues: 125.2952 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 : 1.106 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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= 0.216 Angle : 0.699 8.757 21196 Z= 0.401 Chirality : 0.037 0.162 2391 Planarity : 0.005 0.071 1543 Dihedral : 32.172 179.727 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 *********************** 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 : 1.092 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 97 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8476 (mt-10) REVERT: A 108 ASN cc_start: 0.9550 (t0) cc_final: 0.8971 (t0) REVERT: B 59 LYS cc_start: 0.9447 (tmmt) cc_final: 0.9041 (ttpp) REVERT: B 63 GLU cc_start: 0.8918 (pp20) cc_final: 0.8692 (pp20) REVERT: B 91 LYS cc_start: 0.9620 (tppp) cc_final: 0.9182 (tppp) REVERT: C 25 PHE cc_start: 0.8764 (m-10) cc_final: 0.8504 (m-10) REVERT: C 36 LYS cc_start: 0.9475 (mmpt) cc_final: 0.9137 (mtmm) REVERT: C 89 ASN cc_start: 0.9757 (m-40) cc_final: 0.9491 (m110) REVERT: C 104 GLN cc_start: 0.9079 (mp10) cc_final: 0.8693 (mp10) REVERT: C 111 ILE cc_start: 0.8548 (mm) cc_final: 0.8328 (mm) REVERT: C 112 GLN cc_start: 0.8093 (mp10) cc_final: 0.7657 (mp10) REVERT: D 56 MET cc_start: 0.9152 (tpp) cc_final: 0.8895 (tpp) REVERT: D 80 TYR cc_start: 0.8632 (m-80) cc_final: 0.7918 (m-80) REVERT: D 113 LYS cc_start: 0.9116 (pptt) cc_final: 0.8906 (pptt) REVERT: E 97 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8498 (mt-10) REVERT: E 108 ASN cc_start: 0.9278 (t0) cc_final: 0.8703 (t0) REVERT: F 27 GLN cc_start: 0.9113 (mp10) cc_final: 0.8712 (mp10) REVERT: F 88 TYR cc_start: 0.8636 (m-10) cc_final: 0.8390 (m-10) REVERT: G 56 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8338 (mm-30) REVERT: G 61 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8614 (mm-30) REVERT: G 94 ASN cc_start: 0.9075 (m-40) cc_final: 0.8417 (m110) REVERT: G 112 GLN cc_start: 0.9035 (mp10) cc_final: 0.8491 (mp10) REVERT: H 59 MET cc_start: 0.9330 (mmp) cc_final: 0.9119 (mmm) REVERT: H 65 ASP cc_start: 0.9384 (t0) cc_final: 0.9060 (t0) REVERT: H 80 TYR cc_start: 0.8679 (m-80) cc_final: 0.8212 (m-80) REVERT: H 92 GLN cc_start: 0.9212 (tm130) cc_final: 0.8743 (tm-30) REVERT: H 96 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8308 (ptp-110) outliers start: 10 outliers final: 4 residues processed: 212 average time/residue: 0.3389 time to fit residues: 96.8988 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 : 0.919 ------------------------------------------------------------------------------- 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 58 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 114 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14660 Z= 0.291 Angle : 0.702 9.131 21196 Z= 0.407 Chirality : 0.038 0.184 2391 Planarity : 0.005 0.061 1543 Dihedral : 32.131 179.094 4579 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.05 % Allowed : 15.71 % Favored : 82.24 % 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: -0.09 (0.27), residues: 856 helix: 0.35 (0.21), residues: 559 sheet: -1.02 (1.40), residues: 15 loop : -0.62 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 31 HIS 0.008 0.001 HIS F 75 PHE 0.017 0.002 PHE D 62 TYR 0.058 0.003 TYR B 88 ARG 0.006 0.001 ARG F 95 *********************** 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: 15 poor density : 207 time to evaluate : 1.126 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 67 PHE cc_start: 0.9332 (t80) cc_final: 0.8999 (t80) REVERT: A 108 ASN cc_start: 0.9562 (t0) cc_final: 0.9027 (t0) REVERT: A 120 MET cc_start: 0.8776 (mmm) cc_final: 0.8138 (mmm) REVERT: B 59 LYS cc_start: 0.9486 (tmmt) cc_final: 0.9092 (ttpp) REVERT: B 85 ASP cc_start: 0.8840 (m-30) cc_final: 0.8639 (m-30) REVERT: B 88 TYR cc_start: 0.8763 (m-10) cc_final: 0.8542 (m-80) REVERT: B 91 LYS cc_start: 0.9655 (tppp) cc_final: 0.9174 (tppp) REVERT: C 36 LYS cc_start: 0.9552 (mmpt) cc_final: 0.9306 (mtmm) REVERT: C 89 ASN cc_start: 0.9770 (m-40) cc_final: 0.9429 (m110) REVERT: C 104 GLN cc_start: 0.9154 (mp10) cc_final: 0.8777 (mp10) REVERT: D 56 MET cc_start: 0.9226 (tpp) cc_final: 0.9026 (tpp) REVERT: D 80 TYR cc_start: 0.8451 (m-80) cc_final: 0.8205 (m-80) REVERT: F 27 GLN cc_start: 0.9016 (mp10) cc_final: 0.8757 (mp10) REVERT: F 91 LYS cc_start: 0.9631 (tppt) cc_final: 0.9390 (ttpp) REVERT: G 61 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8683 (mm-30) REVERT: G 94 ASN cc_start: 0.8947 (m-40) cc_final: 0.8235 (m110) REVERT: G 112 GLN cc_start: 0.8946 (mp10) cc_final: 0.8358 (mp10) REVERT: H 56 MET cc_start: 0.8997 (tpt) cc_final: 0.8760 (tpt) REVERT: H 65 ASP cc_start: 0.9411 (t0) cc_final: 0.9066 (t0) REVERT: H 80 TYR cc_start: 0.8629 (m-80) cc_final: 0.8420 (m-80) REVERT: H 92 GLN cc_start: 0.9275 (tm130) cc_final: 0.8967 (tm-30) outliers start: 15 outliers final: 8 residues processed: 211 average time/residue: 0.3503 time to fit residues: 98.6793 Evaluate side-chains 186 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 178 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 104 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3053 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= 0.240 Angle : 0.701 10.357 21196 Z= 0.400 Chirality : 0.037 0.207 2391 Planarity : 0.005 0.060 1543 Dihedral : 31.956 178.944 4579 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.46 % Allowed : 19.40 % Favored : 78.14 % 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: 0.56 (0.21), residues: 558 sheet: -1.36 (1.36), residues: 15 loop : -0.56 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP M 84 HIS 0.005 0.001 HIS M 18 PHE 0.009 0.001 PHE M 17 TYR 0.033 0.002 TYR B 88 ARG 0.010 0.000 ARG D 76 *********************** 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 231 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 1.112 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: 0.9574 (t0) cc_final: 0.8933 (t0) REVERT: B 59 LYS cc_start: 0.9480 (tmmt) cc_final: 0.9212 (ttpp) REVERT: C 36 LYS cc_start: 0.9562 (mmpt) cc_final: 0.9276 (mtmm) REVERT: C 89 ASN cc_start: 0.9761 (m-40) cc_final: 0.9422 (m110) REVERT: C 104 GLN cc_start: 0.9117 (mp10) cc_final: 0.8751 (mp10) REVERT: D 76 ARG cc_start: 0.9366 (ttm110) cc_final: 0.8520 (mtm-85) REVERT: D 102 GLU cc_start: 0.9086 (mp0) cc_final: 0.8855 (tp30) REVERT: F 27 GLN cc_start: 0.9000 (mp10) cc_final: 0.8761 (mp10) REVERT: G 56 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.8720 (mt-10) REVERT: G 61 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8703 (mm-30) REVERT: G 72 ASP cc_start: 0.9203 (m-30) cc_final: 0.9002 (m-30) REVERT: G 89 ASN cc_start: 0.9503 (m-40) cc_final: 0.9021 (p0) REVERT: G 94 ASN cc_start: 0.8948 (m-40) cc_final: 0.8188 (m110) REVERT: G 112 GLN cc_start: 0.8858 (mp10) cc_final: 0.8181 (mp10) REVERT: H 65 ASP cc_start: 0.9354 (t0) cc_final: 0.9069 (t0) REVERT: H 92 GLN cc_start: 0.9349 (OUTLIER) cc_final: 0.9037 (tm-30) outliers start: 18 outliers final: 10 residues processed: 221 average time/residue: 0.3462 time to fit residues: 102.3953 Evaluate side-chains 193 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 F residue 90 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 114 VAL 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 93 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 95 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 80 HIS ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 14660 Z= 0.381 Angle : 0.772 15.557 21196 Z= 0.439 Chirality : 0.041 0.213 2391 Planarity : 0.005 0.056 1543 Dihedral : 32.222 177.658 4579 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.14 % Allowed : 21.72 % Favored : 75.14 % 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: 0.03 (0.27), residues: 856 helix: 0.46 (0.21), residues: 560 sheet: -1.32 (1.44), residues: 15 loop : -0.60 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 88 HIS 0.007 0.002 HIS D 106 PHE 0.017 0.002 PHE A 84 TYR 0.049 0.003 TYR B 88 ARG 0.006 0.001 ARG H 76 *********************** 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 222 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 1.126 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: A 108 ASN cc_start: 0.9553 (t0) cc_final: 0.8992 (t0) REVERT: A 120 MET cc_start: 0.8673 (mmm) cc_final: 0.7984 (mmm) REVERT: B 84 MET cc_start: 0.8976 (tpp) cc_final: 0.8392 (tpp) REVERT: B 88 TYR cc_start: 0.8950 (m-10) cc_final: 0.8229 (m-80) REVERT: B 91 LYS cc_start: 0.9658 (tppp) cc_final: 0.9447 (pttt) REVERT: C 36 LYS cc_start: 0.9626 (mmpt) cc_final: 0.9422 (mtmm) REVERT: C 104 GLN cc_start: 0.9110 (mp10) cc_final: 0.8778 (mp10) REVERT: D 56 MET cc_start: 0.9254 (tpp) cc_final: 0.8941 (tpp) REVERT: D 76 ARG cc_start: 0.9396 (ttm110) cc_final: 0.9113 (mtm-85) REVERT: D 105 LYS cc_start: 0.9438 (mmtt) cc_final: 0.9218 (ptpp) REVERT: E 84 PHE cc_start: 0.9312 (m-80) cc_final: 0.9031 (m-80) REVERT: E 108 ASN cc_start: 0.9535 (t0) cc_final: 0.9181 (t0) REVERT: F 27 GLN cc_start: 0.9081 (mp10) cc_final: 0.8795 (mp10) REVERT: F 88 TYR cc_start: 0.8872 (m-10) cc_final: 0.8355 (m-10) REVERT: G 38 ASN cc_start: 0.8849 (t0) cc_final: 0.8632 (t0) REVERT: G 56 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.8984 (mt-10) REVERT: G 61 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8857 (mm-30) REVERT: G 92 GLU cc_start: 0.8758 (tt0) cc_final: 0.8401 (tt0) REVERT: G 94 ASN cc_start: 0.8881 (m-40) cc_final: 0.8173 (m-40) REVERT: G 112 GLN cc_start: 0.8863 (mp10) cc_final: 0.8268 (mp10) REVERT: H 56 MET cc_start: 0.9189 (tpt) cc_final: 0.8922 (tpt) REVERT: H 65 ASP cc_start: 0.9453 (t0) cc_final: 0.9043 (t0) REVERT: H 76 ARG cc_start: 0.9409 (ttm110) cc_final: 0.9069 (ttp-110) REVERT: H 80 TYR cc_start: 0.8522 (m-10) cc_final: 0.7919 (m-80) REVERT: H 92 GLN cc_start: 0.9423 (OUTLIER) cc_final: 0.9185 (tm-30) outliers start: 23 outliers final: 14 residues processed: 210 average time/residue: 0.3199 time to fit residues: 91.1509 Evaluate side-chains 191 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU 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 124 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 97 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 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 92 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 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 ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14660 Z= 0.283 Angle : 0.735 10.794 21196 Z= 0.418 Chirality : 0.038 0.186 2391 Planarity : 0.005 0.055 1543 Dihedral : 32.079 179.747 4579 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.60 % Allowed : 24.45 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.27), residues: 856 helix: 0.59 (0.21), residues: 560 sheet: -1.38 (1.42), residues: 15 loop : -0.53 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 88 HIS 0.004 0.001 HIS B 75 PHE 0.015 0.001 PHE A 84 TYR 0.042 0.002 TYR B 88 ARG 0.005 0.001 ARG H 76 *********************** 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 223 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 1.105 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: 0.9564 (t0) cc_final: 0.9008 (t0) REVERT: A 120 MET cc_start: 0.8709 (mmm) cc_final: 0.8024 (mmm) REVERT: B 84 MET cc_start: 0.8910 (tpp) cc_final: 0.8313 (tpp) REVERT: B 88 TYR cc_start: 0.8921 (m-10) cc_final: 0.8132 (m-80) REVERT: C 36 LYS cc_start: 0.9623 (mmpt) cc_final: 0.9418 (mtmm) REVERT: C 41 GLU cc_start: 0.8635 (pm20) cc_final: 0.8421 (pm20) REVERT: C 104 GLN cc_start: 0.9044 (mp10) cc_final: 0.8641 (mp10) REVERT: D 73 GLU cc_start: 0.9090 (tp30) cc_final: 0.8481 (tp30) REVERT: D 76 ARG cc_start: 0.9353 (ttm110) cc_final: 0.8093 (ttp-110) REVERT: E 68 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8768 (tm-30) REVERT: E 84 PHE cc_start: 0.9239 (m-80) cc_final: 0.8997 (m-80) REVERT: E 108 ASN cc_start: 0.9546 (t0) cc_final: 0.9169 (t0) REVERT: F 27 GLN cc_start: 0.9013 (mp10) cc_final: 0.8705 (mp10) REVERT: F 31 LYS cc_start: 0.9623 (tmtt) cc_final: 0.9225 (tptp) REVERT: F 79 LYS cc_start: 0.8952 (pttm) cc_final: 0.8644 (pttm) REVERT: F 88 TYR cc_start: 0.8773 (m-10) cc_final: 0.8420 (m-10) REVERT: G 38 ASN cc_start: 0.8780 (t0) cc_final: 0.8511 (t0) REVERT: G 56 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.9007 (mt-10) REVERT: G 61 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8836 (mm-30) REVERT: G 72 ASP cc_start: 0.9178 (m-30) cc_final: 0.8799 (p0) REVERT: G 89 ASN cc_start: 0.9578 (m-40) cc_final: 0.9065 (p0) REVERT: G 112 GLN cc_start: 0.8893 (mp10) cc_final: 0.8328 (mp10) REVERT: H 65 ASP cc_start: 0.9334 (t0) cc_final: 0.9127 (t0) REVERT: H 76 ARG cc_start: 0.9396 (ttm110) cc_final: 0.9107 (ttp-110) REVERT: H 80 TYR cc_start: 0.8308 (m-10) cc_final: 0.7996 (m-80) REVERT: H 82 LYS cc_start: 0.9533 (mmmt) cc_final: 0.9326 (mmmt) REVERT: H 92 GLN cc_start: 0.9438 (tm-30) cc_final: 0.9095 (tm-30) outliers start: 19 outliers final: 9 residues processed: 211 average time/residue: 0.3262 time to fit residues: 93.5856 Evaluate side-chains 193 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 E residue 46 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 62 optimal weight: 0.1980 chunk 111 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- 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** ** E 125 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 M 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4330 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= 0.235 Angle : 0.740 11.489 21196 Z= 0.419 Chirality : 0.038 0.234 2391 Planarity : 0.005 0.057 1543 Dihedral : 31.868 178.562 4579 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.32 % Allowed : 26.09 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.28), residues: 856 helix: 0.61 (0.21), residues: 561 sheet: -1.54 (1.44), residues: 15 loop : -0.39 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 31 HIS 0.004 0.001 HIS F 75 PHE 0.014 0.001 PHE A 84 TYR 0.035 0.002 TYR B 88 ARG 0.009 0.001 ARG G 99 *********************** 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 226 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 1.129 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 108 ASN cc_start: 0.9537 (t0) cc_final: 0.8799 (t0) REVERT: A 115 LYS cc_start: 0.9342 (mmmm) cc_final: 0.9082 (mmmt) REVERT: A 125 GLN cc_start: 0.9252 (mt0) cc_final: 0.8817 (mt0) REVERT: B 31 LYS cc_start: 0.9436 (tptp) cc_final: 0.9224 (tptp) REVERT: B 84 MET cc_start: 0.8880 (tpp) cc_final: 0.8399 (tpp) REVERT: B 88 TYR cc_start: 0.8892 (m-10) cc_final: 0.8252 (m-80) REVERT: C 104 GLN cc_start: 0.8962 (mp10) cc_final: 0.8569 (mp10) REVERT: C 112 GLN cc_start: 0.8522 (mp10) cc_final: 0.7367 (pm20) REVERT: D 73 GLU cc_start: 0.9135 (tp30) cc_final: 0.8869 (tp30) REVERT: D 76 ARG cc_start: 0.9308 (ttm110) cc_final: 0.8555 (ttp-110) REVERT: D 105 LYS cc_start: 0.9171 (mtmm) cc_final: 0.8748 (pttm) REVERT: E 68 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8755 (tm-30) REVERT: E 84 PHE cc_start: 0.9223 (m-80) cc_final: 0.8991 (m-80) REVERT: E 108 ASN cc_start: 0.9501 (t0) cc_final: 0.8936 (t0) REVERT: F 27 GLN cc_start: 0.9016 (mp10) cc_final: 0.8716 (mp10) REVERT: F 79 LYS cc_start: 0.8941 (pttm) cc_final: 0.8680 (pttm) REVERT: F 84 MET cc_start: 0.8758 (tpp) cc_final: 0.8415 (tpp) REVERT: F 88 TYR cc_start: 0.8696 (m-10) cc_final: 0.7512 (m-10) REVERT: G 38 ASN cc_start: 0.8650 (t0) cc_final: 0.8370 (t0) REVERT: G 56 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8780 (mt-10) REVERT: G 61 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8768 (mm-30) REVERT: G 72 ASP cc_start: 0.9159 (m-30) cc_final: 0.8804 (p0) REVERT: G 89 ASN cc_start: 0.9581 (m-40) cc_final: 0.8983 (p0) REVERT: G 92 GLU cc_start: 0.8547 (tt0) cc_final: 0.8102 (tt0) REVERT: G 94 ASN cc_start: 0.8951 (m-40) cc_final: 0.8110 (m110) REVERT: G 112 GLN cc_start: 0.8828 (mp10) cc_final: 0.8172 (mp10) REVERT: H 65 ASP cc_start: 0.9351 (t0) cc_final: 0.9113 (t0) REVERT: H 76 ARG cc_start: 0.9393 (ttm110) cc_final: 0.9092 (ttp-110) REVERT: H 80 TYR cc_start: 0.8319 (m-10) cc_final: 0.7772 (m-80) REVERT: H 92 GLN cc_start: 0.9429 (tm-30) cc_final: 0.9099 (tm-30) REVERT: H 96 ARG cc_start: 0.9217 (ptm-80) cc_final: 0.8999 (ptm-80) outliers start: 17 outliers final: 11 residues processed: 215 average time/residue: 0.3579 time to fit residues: 105.0069 Evaluate side-chains 212 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 E residue 46 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** ** E 125 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** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14660 Z= 0.265 Angle : 0.763 13.224 21196 Z= 0.427 Chirality : 0.039 0.201 2391 Planarity : 0.005 0.056 1543 Dihedral : 31.862 177.628 4579 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.32 % Allowed : 26.91 % Favored : 70.77 % 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: 0.30 (0.28), residues: 856 helix: 0.63 (0.21), residues: 561 sheet: -1.62 (1.44), residues: 15 loop : -0.39 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 31 HIS 0.004 0.001 HIS B 75 PHE 0.012 0.001 PHE A 84 TYR 0.033 0.002 TYR B 88 ARG 0.007 0.001 ARG A 53 *********************** 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 222 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 1.110 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 60 LEU cc_start: 0.9088 (tp) cc_final: 0.8781 (tp) REVERT: A 61 LEU cc_start: 0.9151 (mp) cc_final: 0.8810 (mp) REVERT: A 108 ASN cc_start: 0.9532 (t0) cc_final: 0.8849 (t0) REVERT: A 115 LYS cc_start: 0.9369 (mmmm) cc_final: 0.9124 (mmmt) REVERT: A 125 GLN cc_start: 0.9248 (mt0) cc_final: 0.8806 (mt0) REVERT: B 84 MET cc_start: 0.8821 (tpp) cc_final: 0.8320 (tpp) REVERT: B 88 TYR cc_start: 0.8859 (m-10) cc_final: 0.7974 (m-80) REVERT: C 104 GLN cc_start: 0.8940 (mp10) cc_final: 0.8524 (mp10) REVERT: C 112 GLN cc_start: 0.8296 (mp10) cc_final: 0.7874 (pm20) REVERT: D 73 GLU cc_start: 0.9084 (tp30) cc_final: 0.8800 (tp30) REVERT: D 76 ARG cc_start: 0.9273 (ttm110) cc_final: 0.8669 (ttp-110) REVERT: D 102 GLU cc_start: 0.8772 (tp30) cc_final: 0.8508 (tp30) REVERT: D 105 LYS cc_start: 0.9242 (mtmm) cc_final: 0.8898 (pttm) REVERT: E 68 GLN cc_start: 0.9036 (tm-30) cc_final: 0.8754 (tm-30) REVERT: E 84 PHE cc_start: 0.9251 (m-80) cc_final: 0.9034 (m-80) REVERT: E 97 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8078 (mt-10) REVERT: F 27 GLN cc_start: 0.9025 (mp10) cc_final: 0.8761 (mp10) REVERT: F 79 LYS cc_start: 0.9017 (pttm) cc_final: 0.8659 (pttm) REVERT: F 88 TYR cc_start: 0.8756 (m-10) cc_final: 0.8265 (m-10) REVERT: G 38 ASN cc_start: 0.8704 (t0) cc_final: 0.8382 (t0) REVERT: G 56 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8792 (mt-10) REVERT: G 61 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8848 (mm-30) REVERT: G 72 ASP cc_start: 0.9191 (m-30) cc_final: 0.8886 (p0) REVERT: G 89 ASN cc_start: 0.9598 (m-40) cc_final: 0.9033 (p0) REVERT: G 92 GLU cc_start: 0.8574 (tt0) cc_final: 0.8165 (tt0) REVERT: G 94 ASN cc_start: 0.8961 (m-40) cc_final: 0.8229 (m-40) REVERT: G 112 GLN cc_start: 0.8808 (mp10) cc_final: 0.8232 (mp10) REVERT: H 65 ASP cc_start: 0.9371 (t0) cc_final: 0.9165 (t0) REVERT: H 76 ARG cc_start: 0.9417 (ttm110) cc_final: 0.9149 (ttp-110) REVERT: H 80 TYR cc_start: 0.8334 (m-10) cc_final: 0.7671 (m-80) REVERT: H 92 GLN cc_start: 0.9459 (tm-30) cc_final: 0.9092 (tm-30) outliers start: 17 outliers final: 15 residues processed: 211 average time/residue: 0.3713 time to fit residues: 105.6834 Evaluate side-chains 212 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 61 GLU 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 F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL 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 M residue 123 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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** ** E 125 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** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14660 Z= 0.294 Angle : 0.790 16.653 21196 Z= 0.438 Chirality : 0.039 0.201 2391 Planarity : 0.005 0.054 1543 Dihedral : 31.940 178.195 4579 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.73 % Allowed : 26.09 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.28), residues: 856 helix: 0.55 (0.21), residues: 561 sheet: -1.67 (1.43), residues: 15 loop : -0.43 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 88 HIS 0.006 0.001 HIS B 75 PHE 0.012 0.002 PHE A 84 TYR 0.036 0.002 TYR B 88 ARG 0.004 0.001 ARG H 96 *********************** 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 225 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 1.179 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 108 ASN cc_start: 0.9543 (t0) cc_final: 0.8877 (t0) REVERT: A 115 LYS cc_start: 0.9392 (mmmm) cc_final: 0.9135 (mmmt) REVERT: A 125 GLN cc_start: 0.9236 (mt0) cc_final: 0.8772 (mt0) REVERT: C 104 GLN cc_start: 0.8927 (mp10) cc_final: 0.8520 (mp10) REVERT: D 73 GLU cc_start: 0.9100 (tp30) cc_final: 0.8853 (tp30) REVERT: D 76 ARG cc_start: 0.9300 (ttm110) cc_final: 0.8798 (ttp-110) REVERT: D 105 LYS cc_start: 0.9247 (mtmm) cc_final: 0.8919 (ptpp) REVERT: E 84 PHE cc_start: 0.9258 (m-80) cc_final: 0.9056 (m-80) REVERT: E 122 LYS cc_start: 0.9366 (ptmm) cc_final: 0.9163 (ptmm) REVERT: F 27 GLN cc_start: 0.9051 (mp10) cc_final: 0.8808 (mp10) REVERT: F 31 LYS cc_start: 0.9591 (tmtt) cc_final: 0.9168 (tptp) REVERT: F 79 LYS cc_start: 0.8999 (pttm) cc_final: 0.8654 (pttm) REVERT: F 84 MET cc_start: 0.8746 (tpp) cc_final: 0.8486 (tpp) REVERT: F 88 TYR cc_start: 0.8771 (m-10) cc_final: 0.8048 (m-10) REVERT: G 38 ASN cc_start: 0.8812 (t0) cc_final: 0.8437 (t0) REVERT: G 56 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8786 (mt-10) REVERT: G 61 GLU cc_start: 0.9280 (mm-30) cc_final: 0.8868 (mm-30) REVERT: G 72 ASP cc_start: 0.9247 (m-30) cc_final: 0.8882 (p0) REVERT: G 94 ASN cc_start: 0.8970 (m-40) cc_final: 0.8241 (m-40) REVERT: G 112 GLN cc_start: 0.8794 (mp10) cc_final: 0.8236 (mp10) REVERT: H 65 ASP cc_start: 0.9381 (t0) cc_final: 0.9144 (t0) REVERT: H 76 ARG cc_start: 0.9432 (ttm110) cc_final: 0.9108 (ttp-110) REVERT: H 92 GLN cc_start: 0.9476 (tm-30) cc_final: 0.9135 (tm-30) outliers start: 20 outliers final: 14 residues processed: 214 average time/residue: 0.3574 time to fit residues: 103.9676 Evaluate side-chains 210 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 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 74 GLU Chi-restraints excluded: chain F residue 86 VAL 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 M residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 chunk 98 optimal weight: 8.9990 chunk 28 optimal weight: 0.5980 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 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** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14660 Z= 0.327 Angle : 0.831 16.189 21196 Z= 0.456 Chirality : 0.040 0.204 2391 Planarity : 0.005 0.053 1543 Dihedral : 32.036 179.031 4579 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.46 % Allowed : 26.64 % Favored : 70.90 % 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: 0.14 (0.28), residues: 856 helix: 0.55 (0.22), residues: 559 sheet: -1.74 (1.43), residues: 15 loop : -0.52 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 88 HIS 0.005 0.001 HIS D 79 PHE 0.012 0.002 PHE A 104 TYR 0.064 0.003 TYR B 88 ARG 0.005 0.001 ARG D 76 ********************** 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: 18 poor density : 199 time to evaluate : 1.147 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 108 ASN cc_start: 0.9552 (t0) cc_final: 0.8896 (t0) REVERT: A 115 LYS cc_start: 0.9440 (mmmm) cc_final: 0.9174 (mmmt) REVERT: A 122 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.9022 (ptpp) REVERT: A 125 GLN cc_start: 0.9195 (mt0) cc_final: 0.8775 (mt0) REVERT: B 88 TYR cc_start: 0.9081 (m-80) cc_final: 0.8020 (m-80) REVERT: C 104 GLN cc_start: 0.8921 (mp10) cc_final: 0.8525 (mp10) REVERT: D 73 GLU cc_start: 0.9107 (tp30) cc_final: 0.8900 (tp30) REVERT: D 76 ARG cc_start: 0.9181 (ttm110) cc_final: 0.8877 (ttp-110) REVERT: D 102 GLU cc_start: 0.8790 (tp30) cc_final: 0.8574 (tp30) REVERT: D 105 LYS cc_start: 0.9273 (mtmm) cc_final: 0.8998 (ptpp) REVERT: E 97 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8098 (mt-10) REVERT: E 122 LYS cc_start: 0.9392 (ptmm) cc_final: 0.9171 (ptmm) REVERT: F 27 GLN cc_start: 0.9075 (mp10) cc_final: 0.8826 (mp10) REVERT: F 63 GLU cc_start: 0.9333 (OUTLIER) cc_final: 0.9072 (pm20) REVERT: F 79 LYS cc_start: 0.9009 (pttm) cc_final: 0.8729 (pttm) REVERT: G 38 ASN cc_start: 0.8887 (t0) cc_final: 0.8549 (t0) REVERT: G 56 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8800 (mt-10) REVERT: G 61 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8931 (mm-30) REVERT: G 72 ASP cc_start: 0.9333 (m-30) cc_final: 0.8968 (p0) REVERT: G 89 ASN cc_start: 0.9656 (m110) cc_final: 0.9340 (p0) REVERT: G 112 GLN cc_start: 0.8825 (mp10) cc_final: 0.8291 (mp10) REVERT: H 76 ARG cc_start: 0.9429 (ttm110) cc_final: 0.9108 (ttp-110) REVERT: H 92 GLN cc_start: 0.9478 (tm-30) cc_final: 0.9166 (tm-30) outliers start: 18 outliers final: 13 residues processed: 205 average time/residue: 0.3357 time to fit residues: 93.3575 Evaluate side-chains 208 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LYS 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 61 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 86 VAL 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 M residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 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 = 0.046262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.031555 restraints weight = 99854.321| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.86 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14660 Z= 0.233 Angle : 0.820 16.917 21196 Z= 0.447 Chirality : 0.039 0.204 2391 Planarity : 0.005 0.058 1543 Dihedral : 31.709 179.659 4579 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.78 % Allowed : 28.55 % 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: 0.17 (0.28), residues: 856 helix: 0.54 (0.22), residues: 560 sheet: -1.71 (1.41), residues: 15 loop : -0.44 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 31 HIS 0.004 0.001 HIS B 75 PHE 0.013 0.002 PHE A 84 TYR 0.052 0.003 TYR B 88 ARG 0.004 0.000 ARG H 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2813.32 seconds wall clock time: 52 minutes 6.89 seconds (3126.89 seconds total)