Starting phenix.real_space_refine on Mon Sep 23 19:33:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hu7_0273/09_2024/6hu7_0273.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hu7_0273/09_2024/6hu7_0273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hu7_0273/09_2024/6hu7_0273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hu7_0273/09_2024/6hu7_0273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hu7_0273/09_2024/6hu7_0273.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hu7_0273/09_2024/6hu7_0273.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.079 sd= 1.306 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 3155 2.51 5 N 820 2.21 5 O 888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4890 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1218 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 12, 'TRANS': 139} Chain: "A" Number of atoms: 1190 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 147, 1171 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 12, 'TRANS': 134} Conformer: "B" Number of residues, atoms: 147, 1171 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 12, 'TRANS': 134} bond proxies already assigned to first conformer: 1185 Chain: "C" Number of atoms: 1218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 151, 1207 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 12, 'TRANS': 138} Conformer: "B" Number of residues, atoms: 151, 1207 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 12, 'TRANS': 138} bond proxies already assigned to first conformer: 1230 Chain: "D" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1207 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 12, 'TRANS': 138} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "H" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 127 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 127 " occ=0.50 residue: pdb=" N AARG C 82 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 82 " occ=0.50 Time building chain proxies: 7.06, per 1000 atoms: 1.44 Number of scatterers: 4890 At special positions: 0 Unit cell: (107.712, 117.216, 81.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 888 8.00 N 820 7.00 C 3155 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: 1.11 Conformation dependent library (CDL) restraints added in 776.6 milliseconds 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1176 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 0 sheets defined 73.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'B' and resid 6 through 10 Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 18 through 19 No H-bonds generated for 'chain 'B' and resid 18 through 19' Processing helix chain 'B' and resid 20 through 24 Processing helix chain 'B' and resid 26 through 43 removed outlier: 3.585A pdb=" N ARG B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLU B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ALA B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 75 removed outlier: 3.718A pdb=" N GLY B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 110 removed outlier: 3.654A pdb=" N ASP B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY B 94 " --> pdb=" O ASN B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 128 Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 20 through 24 removed outlier: 3.822A pdb=" N PHE A 24 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 38 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 49 through 76 removed outlier: 3.545A pdb=" N LEU A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 111 removed outlier: 3.507A pdb=" N ASP A 83 " --> pdb=" O PRO A 79 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 100 " --> pdb=" O LYS A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 128 Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 12 through 17 removed outlier: 3.588A pdb=" N LEU C 16 " --> pdb=" O THR C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 43 removed outlier: 3.639A pdb=" N ARG C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ALA C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 76 Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.523A pdb=" N LEU C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 111 removed outlier: 3.831A pdb=" N LYS C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 128 removed outlier: 3.573A pdb=" N ARG C 127 " --> pdb=" O GLY C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 20 through 24 removed outlier: 3.760A pdb=" N PHE D 24 " --> pdb=" O SER D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 38 Processing helix chain 'D' and resid 38 through 43 Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.553A pdb=" N GLY D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.505A pdb=" N ASP D 83 " --> pdb=" O PRO D 79 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 109 removed outlier: 4.131A pdb=" N LYS D 96 " --> pdb=" O ASN D 92 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 97 " --> pdb=" O MET D 93 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 128 removed outlier: 3.570A pdb=" N THR D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) 299 hydrogen bonds defined for protein. 857 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1564 1.34 - 1.46: 1067 1.46 - 1.57: 2360 1.57 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 5030 Sorted by residual: bond pdb=" CG LEU A 97 " pdb=" CD2 LEU A 97 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.58e+00 bond pdb=" CG LEU C 30 " pdb=" CD1 LEU C 30 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.16e+00 bond pdb=" CG LEU D 97 " pdb=" CD2 LEU D 97 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.78e+00 bond pdb=" CB GLU B 8 " pdb=" CG GLU B 8 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.11e+00 bond pdb=" CB ARG A 98 " pdb=" CG ARG A 98 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.04e+00 ... (remaining 5025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 6611 1.80 - 3.61: 238 3.61 - 5.41: 25 5.41 - 7.21: 7 7.21 - 9.02: 3 Bond angle restraints: 6884 Sorted by residual: angle pdb=" CA TYR A 38 " pdb=" CB TYR A 38 " pdb=" CG TYR A 38 " ideal model delta sigma weight residual 113.90 107.49 6.41 1.80e+00 3.09e-01 1.27e+01 angle pdb=" CA TYR C 132 " pdb=" CB TYR C 132 " pdb=" CG TYR C 132 " ideal model delta sigma weight residual 113.90 108.31 5.59 1.80e+00 3.09e-01 9.65e+00 angle pdb=" CA TYR D 38 " pdb=" CB TYR D 38 " pdb=" CG TYR D 38 " ideal model delta sigma weight residual 113.90 108.53 5.37 1.80e+00 3.09e-01 8.89e+00 angle pdb=" C VAL C 148 " pdb=" N VAL C 149 " pdb=" CA VAL C 149 " ideal model delta sigma weight residual 121.97 126.98 -5.01 1.80e+00 3.09e-01 7.75e+00 angle pdb=" C MET D 1 " pdb=" N ASP D 2 " pdb=" CA ASP D 2 " ideal model delta sigma weight residual 122.46 126.24 -3.78 1.41e+00 5.03e-01 7.20e+00 ... (remaining 6879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.70: 2873 15.70 - 31.39: 92 31.39 - 47.08: 27 47.08 - 62.78: 1 62.78 - 78.47: 5 Dihedral angle restraints: 2998 sinusoidal: 1194 harmonic: 1804 Sorted by residual: dihedral pdb=" CA LEU A 143 " pdb=" C LEU A 143 " pdb=" N PRO A 144 " pdb=" CA PRO A 144 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA LEU D 108 " pdb=" C LEU D 108 " pdb=" N THR D 109 " pdb=" CA THR D 109 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LEU B 143 " pdb=" C LEU B 143 " pdb=" N PRO B 144 " pdb=" CA PRO B 144 " ideal model delta harmonic sigma weight residual 180.00 160.98 19.02 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 2995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 537 0.047 - 0.094: 203 0.094 - 0.141: 42 0.141 - 0.187: 7 0.187 - 0.234: 1 Chirality restraints: 790 Sorted by residual: chirality pdb=" CG LEU A 97 " pdb=" CB LEU A 97 " pdb=" CD1 LEU A 97 " pdb=" CD2 LEU A 97 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA HIS A 47 " pdb=" N HIS A 47 " pdb=" C HIS A 47 " pdb=" CB HIS A 47 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CB THR D 109 " pdb=" CA THR D 109 " pdb=" OG1 THR D 109 " pdb=" CG2 THR D 109 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.39e-01 ... (remaining 787 not shown) Planarity restraints: 872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 18 " -0.026 2.00e-02 2.50e+03 2.28e-02 9.12e+00 pdb=" CG PHE C 18 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE C 18 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 18 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 18 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 18 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 18 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 132 " 0.025 2.00e-02 2.50e+03 2.05e-02 8.44e+00 pdb=" CG TYR C 132 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR C 132 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR C 132 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 132 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 132 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 132 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 132 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 38 " -0.028 2.00e-02 2.50e+03 1.89e-02 7.11e+00 pdb=" CG TYR A 38 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 38 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 38 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 38 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 38 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 38 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 38 " -0.006 2.00e-02 2.50e+03 ... (remaining 869 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 71 2.68 - 3.24: 4989 3.24 - 3.79: 7768 3.79 - 4.35: 10897 4.35 - 4.90: 17311 Nonbonded interactions: 41036 Sorted by model distance: nonbonded pdb=" NH1 ARG B 150 " pdb=" O LEU C 143 " model vdw 2.130 3.120 nonbonded pdb=" OD1 ASP A 2 " pdb=" N ILE A 3 " model vdw 2.165 3.120 nonbonded pdb=" O THR B 146 " pdb=" OG1 THR B 147 " model vdw 2.273 3.040 nonbonded pdb=" O PHE D 24 " pdb=" NH1 ARG D 98 " model vdw 2.283 3.120 nonbonded pdb=" OD1 ASP A 83 " pdb=" N LEU A 84 " model vdw 2.314 3.120 ... (remaining 41031 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 1 through 27 or resid 29 through 81 or resid 83 through 12 \ 6 or resid 128 through 147)) selection = (chain 'B' and (resid 1 through 27 or resid 29 through 81 or resid 83 through 12 \ 6 or resid 128 through 147)) selection = (chain 'C' and (resid 1 through 27 or resid 29 through 81 or resid 83 through 12 \ 6 or resid 128 through 147)) selection = (chain 'D' and (resid 1 through 27 or resid 29 through 81 or resid 83 through 12 \ 6 or resid 128 through 147)) } ncs_group { reference = chain 'G' selection = chain 'H' } 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=0.50 max=1.00 mean=0.99 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: 8.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.080 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 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 : 0.008 0.071 5030 Z= 0.520 Angle : 0.781 9.018 6884 Z= 0.411 Chirality : 0.050 0.234 790 Planarity : 0.007 0.060 872 Dihedral : 9.806 78.470 1822 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.50 % Allowed : 2.69 % Favored : 96.81 % Rotamer: Outliers : 0.36 % Allowed : 0.36 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.28), residues: 602 helix: -3.23 (0.16), residues: 405 sheet: None (None), residues: 0 loop : 0.50 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 102 HIS 0.014 0.004 HIS A 47 PHE 0.053 0.003 PHE C 18 TYR 0.050 0.006 TYR C 132 ARG 0.011 0.002 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.550 Fit side-chains REVERT: B 61 CYS cc_start: 0.8966 (t) cc_final: 0.8723 (t) REVERT: B 82 ARG cc_start: 0.6554 (mtp180) cc_final: 0.5565 (ptt-90) REVERT: B 117 GLU cc_start: 0.8095 (tt0) cc_final: 0.7722 (tp30) REVERT: A 64 GLU cc_start: 0.6708 (tp30) cc_final: 0.6467 (mm-30) REVERT: A 117 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8486 (mm-30) REVERT: A 141 SER cc_start: 0.8697 (m) cc_final: 0.8441 (m) REVERT: C 83 ASP cc_start: 0.7576 (m-30) cc_final: 0.7194 (m-30) REVERT: C 113 GLU cc_start: 0.7977 (pm20) cc_final: 0.7764 (mp0) REVERT: D 64 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7845 (mm-30) REVERT: D 78 ASP cc_start: 0.7218 (t0) cc_final: 0.6891 (t0) REVERT: D 96 LYS cc_start: 0.8524 (mtpp) cc_final: 0.8281 (mtpt) REVERT: D 136 ASN cc_start: 0.7122 (p0) cc_final: 0.6851 (p0) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 1.4468 time to fit residues: 180.5753 Evaluate side-chains 95 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 HIS B 57 GLN B 75 ASN B 90 ASN B 104 HIS A 47 HIS A 52 HIS A 57 GLN A 75 ASN A 136 ASN C 52 HIS C 75 ASN D 47 HIS D 52 HIS D 90 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5030 Z= 0.223 Angle : 0.673 9.158 6884 Z= 0.341 Chirality : 0.042 0.239 790 Planarity : 0.007 0.044 872 Dihedral : 5.209 23.067 670 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.50 % Allowed : 1.68 % Favored : 97.82 % Rotamer: Outliers : 2.01 % Allowed : 8.21 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.33), residues: 602 helix: -0.19 (0.24), residues: 406 sheet: None (None), residues: 0 loop : 1.22 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 102 HIS 0.006 0.002 HIS B 47 PHE 0.032 0.002 PHE C 18 TYR 0.028 0.003 TYR C 132 ARG 0.008 0.001 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.558 Fit side-chains REVERT: B 61 CYS cc_start: 0.8738 (t) cc_final: 0.8515 (t) REVERT: B 76 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.5938 (tt) REVERT: B 117 GLU cc_start: 0.8024 (tt0) cc_final: 0.7630 (mm-30) REVERT: A 8 GLU cc_start: 0.8596 (pt0) cc_final: 0.8302 (pt0) REVERT: A 32 ASP cc_start: 0.8741 (m-30) cc_final: 0.8482 (m-30) REVERT: A 75 ASN cc_start: 0.7096 (m110) cc_final: 0.6801 (m110) REVERT: A 79 PRO cc_start: 0.7631 (Cg_endo) cc_final: 0.7415 (Cg_exo) REVERT: C 113 GLU cc_start: 0.8023 (pm20) cc_final: 0.7748 (mp0) REVERT: D 64 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7644 (mm-30) REVERT: D 98 ARG cc_start: 0.8256 (ptt90) cc_final: 0.7988 (ptt-90) outliers start: 9 outliers final: 3 residues processed: 106 average time/residue: 1.3880 time to fit residues: 152.0024 Evaluate side-chains 94 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 142 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 0.0670 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 43 optimal weight: 0.0050 chunk 40 optimal weight: 1.9990 overall best weight: 0.5734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5030 Z= 0.171 Angle : 0.577 8.798 6884 Z= 0.286 Chirality : 0.038 0.201 790 Planarity : 0.005 0.039 872 Dihedral : 4.725 20.704 670 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.50 % Allowed : 1.51 % Favored : 97.98 % Rotamer: Outliers : 1.46 % Allowed : 10.58 % Favored : 87.96 % 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: 1.69 (0.34), residues: 602 helix: 1.15 (0.25), residues: 409 sheet: None (None), residues: 0 loop : 1.41 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 102 HIS 0.002 0.001 HIS B 104 PHE 0.023 0.001 PHE C 18 TYR 0.021 0.002 TYR C 132 ARG 0.003 0.000 ARG C 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.534 Fit side-chains REVERT: B 61 CYS cc_start: 0.8711 (t) cc_final: 0.8489 (t) REVERT: B 76 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6139 (tt) REVERT: B 117 GLU cc_start: 0.7845 (tt0) cc_final: 0.7531 (mm-30) REVERT: B 145 GLU cc_start: 0.5669 (mp0) cc_final: 0.5438 (mm-30) REVERT: A 46 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7779 (mm-30) REVERT: A 75 ASN cc_start: 0.6959 (m110) cc_final: 0.6625 (m110) REVERT: A 77 GLU cc_start: 0.5759 (mp0) cc_final: 0.5518 (mm-30) REVERT: C 28 ARG cc_start: 0.7976 (mmm160) cc_final: 0.7329 (mmm160) REVERT: C 32 ASP cc_start: 0.8596 (m-30) cc_final: 0.8285 (m-30) REVERT: D 64 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7650 (mm-30) REVERT: D 98 ARG cc_start: 0.8037 (ptt90) cc_final: 0.7822 (ptt-90) outliers start: 6 outliers final: 2 residues processed: 95 average time/residue: 1.3854 time to fit residues: 136.0595 Evaluate side-chains 90 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain D residue 93 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN A 104 HIS A 136 ASN D 104 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5030 Z= 0.190 Angle : 0.571 8.513 6884 Z= 0.282 Chirality : 0.039 0.199 790 Planarity : 0.005 0.036 872 Dihedral : 4.511 18.813 670 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.50 % Allowed : 1.85 % Favored : 97.65 % Rotamer: Outliers : 2.01 % Allowed : 10.95 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.34), residues: 602 helix: 1.58 (0.26), residues: 410 sheet: None (None), residues: 0 loop : 1.48 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 62 HIS 0.006 0.001 HIS B 47 PHE 0.022 0.001 PHE C 18 TYR 0.022 0.002 TYR C 132 ARG 0.003 0.000 ARG C 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.557 Fit side-chains REVERT: B 14 GLU cc_start: 0.8889 (mp0) cc_final: 0.8509 (mt-10) REVERT: B 61 CYS cc_start: 0.8739 (t) cc_final: 0.8500 (t) REVERT: B 76 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6135 (tt) REVERT: B 117 GLU cc_start: 0.7907 (tt0) cc_final: 0.7604 (mm-30) REVERT: A 75 ASN cc_start: 0.6931 (m110) cc_final: 0.6603 (m110) REVERT: A 77 GLU cc_start: 0.5699 (mp0) cc_final: 0.5438 (mm-30) REVERT: D 40 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7771 (tp30) REVERT: D 64 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7607 (mm-30) REVERT: D 98 ARG cc_start: 0.8021 (ptt90) cc_final: 0.7807 (ptt-90) outliers start: 9 outliers final: 5 residues processed: 97 average time/residue: 1.4107 time to fit residues: 141.6084 Evaluate side-chains 91 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 143 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5030 Z= 0.166 Angle : 0.552 7.883 6884 Z= 0.271 Chirality : 0.038 0.176 790 Planarity : 0.005 0.036 872 Dihedral : 4.359 17.266 670 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.50 % Allowed : 1.85 % Favored : 97.65 % Rotamer: Outliers : 2.01 % Allowed : 11.86 % Favored : 86.13 % 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: 2.56 (0.35), residues: 602 helix: 1.85 (0.26), residues: 410 sheet: None (None), residues: 0 loop : 1.64 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 62 HIS 0.003 0.001 HIS B 104 PHE 0.019 0.001 PHE C 18 TYR 0.019 0.001 TYR C 132 ARG 0.003 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.590 Fit side-chains REVERT: B 14 GLU cc_start: 0.8902 (mp0) cc_final: 0.8480 (mt-10) REVERT: B 61 CYS cc_start: 0.8741 (t) cc_final: 0.8488 (t) REVERT: B 76 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6036 (tt) REVERT: A 75 ASN cc_start: 0.6949 (m110) cc_final: 0.6662 (m110) REVERT: A 77 GLU cc_start: 0.5737 (mp0) cc_final: 0.5467 (mm-30) REVERT: C 32 ASP cc_start: 0.8670 (m-30) cc_final: 0.8432 (m-30) REVERT: D 64 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7602 (mm-30) outliers start: 9 outliers final: 5 residues processed: 97 average time/residue: 1.5462 time to fit residues: 154.7580 Evaluate side-chains 88 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 146 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5030 Z= 0.173 Angle : 0.555 7.631 6884 Z= 0.271 Chirality : 0.038 0.166 790 Planarity : 0.005 0.035 872 Dihedral : 4.271 16.131 670 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.18 % Favored : 97.48 % Rotamer: Outliers : 2.55 % Allowed : 12.04 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.35), residues: 602 helix: 1.96 (0.26), residues: 411 sheet: None (None), residues: 0 loop : 1.63 (0.46), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 62 HIS 0.004 0.001 HIS B 104 PHE 0.019 0.001 PHE C 18 TYR 0.019 0.001 TYR C 132 ARG 0.003 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.523 Fit side-chains REVERT: B 14 GLU cc_start: 0.8915 (mp0) cc_final: 0.8581 (mt-10) REVERT: B 61 CYS cc_start: 0.8749 (t) cc_final: 0.8484 (t) REVERT: B 76 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.5976 (tt) REVERT: B 97 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8567 (tm) REVERT: A 75 ASN cc_start: 0.6995 (m110) cc_final: 0.6703 (m110) REVERT: A 77 GLU cc_start: 0.5731 (mp0) cc_final: 0.5459 (mm-30) REVERT: C 28 ARG cc_start: 0.7953 (mmm160) cc_final: 0.7420 (mmm160) REVERT: D 64 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7592 (mm-30) outliers start: 12 outliers final: 4 residues processed: 97 average time/residue: 1.3786 time to fit residues: 138.2265 Evaluate side-chains 88 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 146 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 0.0170 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5030 Z= 0.171 Angle : 0.561 8.093 6884 Z= 0.274 Chirality : 0.038 0.168 790 Planarity : 0.005 0.034 872 Dihedral : 4.219 15.084 670 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.18 % Favored : 97.48 % Rotamer: Outliers : 1.82 % Allowed : 12.41 % Favored : 85.77 % 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: 2.76 (0.35), residues: 602 helix: 2.04 (0.26), residues: 410 sheet: None (None), residues: 0 loop : 1.61 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 62 HIS 0.003 0.001 HIS B 104 PHE 0.017 0.001 PHE C 18 TYR 0.018 0.001 TYR C 132 ARG 0.004 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.712 Fit side-chains REVERT: B 14 GLU cc_start: 0.8744 (mp0) cc_final: 0.8512 (mt-10) REVERT: B 61 CYS cc_start: 0.8744 (t) cc_final: 0.8486 (t) REVERT: B 76 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6177 (tt) REVERT: B 97 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8607 (tm) REVERT: A 75 ASN cc_start: 0.6976 (m110) cc_final: 0.6698 (m110) REVERT: A 77 GLU cc_start: 0.5851 (mp0) cc_final: 0.5595 (mm-30) REVERT: C 28 ARG cc_start: 0.7894 (mmm160) cc_final: 0.7043 (tpm170) outliers start: 8 outliers final: 5 residues processed: 95 average time/residue: 1.6259 time to fit residues: 159.0856 Evaluate side-chains 93 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 146 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 0.0870 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5030 Z= 0.166 Angle : 0.561 8.298 6884 Z= 0.275 Chirality : 0.038 0.162 790 Planarity : 0.005 0.034 872 Dihedral : 4.166 14.685 670 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.35 % Favored : 97.31 % Rotamer: Outliers : 2.01 % Allowed : 13.14 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.35), residues: 602 helix: 2.09 (0.26), residues: 410 sheet: None (None), residues: 0 loop : 1.59 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 62 HIS 0.003 0.001 HIS B 104 PHE 0.017 0.001 PHE C 18 TYR 0.017 0.001 TYR C 132 ARG 0.003 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.555 Fit side-chains REVERT: B 61 CYS cc_start: 0.8747 (t) cc_final: 0.8491 (t) REVERT: B 76 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6158 (tt) REVERT: A 75 ASN cc_start: 0.6962 (m110) cc_final: 0.6699 (m110) REVERT: A 77 GLU cc_start: 0.5755 (mp0) cc_final: 0.5508 (mm-30) REVERT: C 28 ARG cc_start: 0.7959 (mmm160) cc_final: 0.7262 (tpm170) outliers start: 9 outliers final: 5 residues processed: 93 average time/residue: 1.4907 time to fit residues: 143.2970 Evaluate side-chains 91 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 146 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 16 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5030 Z= 0.166 Angle : 0.566 8.510 6884 Z= 0.276 Chirality : 0.038 0.167 790 Planarity : 0.005 0.033 872 Dihedral : 4.129 14.350 670 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.18 % Favored : 97.48 % Rotamer: Outliers : 1.46 % Allowed : 14.05 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.35), residues: 602 helix: 2.09 (0.26), residues: 412 sheet: None (None), residues: 0 loop : 1.67 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 62 HIS 0.003 0.001 HIS B 104 PHE 0.017 0.001 PHE C 18 TYR 0.017 0.001 TYR C 132 ARG 0.002 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.649 Fit side-chains REVERT: B 8 GLU cc_start: 0.8742 (tt0) cc_final: 0.8497 (tt0) REVERT: B 61 CYS cc_start: 0.8745 (t) cc_final: 0.8500 (t) REVERT: B 76 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6127 (tt) REVERT: B 83 ASP cc_start: 0.8013 (m-30) cc_final: 0.7192 (p0) REVERT: A 75 ASN cc_start: 0.6951 (m110) cc_final: 0.6698 (m110) REVERT: A 77 GLU cc_start: 0.5699 (mp0) cc_final: 0.5465 (mm-30) REVERT: C 28 ARG cc_start: 0.7940 (mmm160) cc_final: 0.7351 (tpm170) outliers start: 6 outliers final: 5 residues processed: 91 average time/residue: 1.4846 time to fit residues: 139.6954 Evaluate side-chains 90 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 146 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 36 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5030 Z= 0.150 Angle : 0.552 8.642 6884 Z= 0.269 Chirality : 0.037 0.164 790 Planarity : 0.004 0.033 872 Dihedral : 4.059 14.127 670 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.18 % Favored : 97.48 % Rotamer: Outliers : 1.46 % Allowed : 14.42 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.35), residues: 602 helix: 2.16 (0.26), residues: 412 sheet: None (None), residues: 0 loop : 1.69 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 62 HIS 0.003 0.001 HIS B 104 PHE 0.015 0.001 PHE C 18 TYR 0.015 0.001 TYR C 132 ARG 0.002 0.000 ARG C 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.551 Fit side-chains REVERT: B 61 CYS cc_start: 0.8723 (t) cc_final: 0.8490 (t) REVERT: B 76 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6166 (tt) REVERT: B 83 ASP cc_start: 0.8015 (m-30) cc_final: 0.7206 (p0) REVERT: A 75 ASN cc_start: 0.6918 (m110) cc_final: 0.6689 (m110) REVERT: A 77 GLU cc_start: 0.5677 (mp0) cc_final: 0.5449 (mm-30) REVERT: A 96 LYS cc_start: 0.8484 (tppp) cc_final: 0.8216 (tppp) REVERT: C 28 ARG cc_start: 0.7947 (mmm160) cc_final: 0.7399 (tpm170) REVERT: C 66 MET cc_start: 0.8217 (mmm) cc_final: 0.7984 (mmp) outliers start: 6 outliers final: 4 residues processed: 94 average time/residue: 1.3475 time to fit residues: 131.1671 Evaluate side-chains 92 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 146 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 HIS B 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.116865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.101251 restraints weight = 14385.810| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.86 r_work: 0.3034 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5030 Z= 0.180 Angle : 0.564 8.277 6884 Z= 0.276 Chirality : 0.038 0.161 790 Planarity : 0.005 0.033 872 Dihedral : 4.080 14.408 670 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.02 % Favored : 97.65 % Rotamer: Outliers : 1.46 % Allowed : 14.60 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.35), residues: 602 helix: 2.17 (0.26), residues: 412 sheet: None (None), residues: 0 loop : 1.68 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 62 HIS 0.004 0.001 HIS B 47 PHE 0.017 0.001 PHE C 18 TYR 0.018 0.002 TYR C 132 ARG 0.002 0.000 ARG A 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3183.72 seconds wall clock time: 56 minutes 33.89 seconds (3393.89 seconds total)