Starting phenix.real_space_refine on Tue Feb 13 11:17:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n62_24192/02_2024/7n62_24192_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n62_24192/02_2024/7n62_24192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n62_24192/02_2024/7n62_24192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n62_24192/02_2024/7n62_24192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n62_24192/02_2024/7n62_24192_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n62_24192/02_2024/7n62_24192_neut.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 3569 2.51 5 N 933 2.21 5 O 1094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "L GLU 165": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5613 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2235 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 14, 'TRANS': 262} Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1689 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "L" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1619 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.50, per 1000 atoms: 0.62 Number of scatterers: 5613 At special positions: 0 Unit cell: (64.35, 95.7, 122.925, 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 17 16.00 O 1094 8.00 N 933 7.00 C 3569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 971.0 milliseconds 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1314 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 16 sheets defined 5.3% alpha, 35.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.558A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 195 through 199 Processing helix chain 'L' and resid 29 through 32 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.775A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 182 through 188 removed outlier: 4.097A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 3.628A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.649A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 5.651A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 Processing sheet with id=AA6, first strand: chain 'A' and resid 144 through 145 removed outlier: 4.062A pdb=" N TYR A 144 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.865A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 132 through 133 removed outlier: 4.376A pdb=" N LEU H 148 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL H 192 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 132 through 133 removed outlier: 4.376A pdb=" N LEU H 148 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL H 192 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER H 187 " --> pdb=" O VAL H 179 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 161 through 164 Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.530A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.631A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.731A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS L 194 " --> pdb=" O LYS L 207 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) 180 hydrogen bonds defined for protein. 429 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: 1.78 Time building geometry restraints manager: 2.22 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: 1779 1.34 - 1.46: 1526 1.46 - 1.59: 2431 1.59 - 1.71: 0 1.71 - 1.83: 22 Bond restraints: 5758 Sorted by residual: bond pdb=" N GLU H 6 " pdb=" CA GLU H 6 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.23e-02 6.61e+03 6.33e+00 bond pdb=" N ASP A 253 " pdb=" CA ASP A 253 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.50e-02 4.44e+03 5.06e+00 bond pdb=" C ALA H 92 " pdb=" N VAL H 93 " ideal model delta sigma weight residual 1.334 1.313 0.021 1.24e-02 6.50e+03 2.83e+00 bond pdb=" CB PRO H 159 " pdb=" CG PRO H 159 " ideal model delta sigma weight residual 1.506 1.567 -0.061 3.90e-02 6.57e+02 2.41e+00 bond pdb=" CB TRP H 36 " pdb=" CG TRP H 36 " ideal model delta sigma weight residual 1.498 1.455 0.043 3.10e-02 1.04e+03 1.97e+00 ... (remaining 5753 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.47: 164 106.47 - 113.36: 3129 113.36 - 120.25: 1921 120.25 - 127.14: 2556 127.14 - 134.02: 62 Bond angle restraints: 7832 Sorted by residual: angle pdb=" C GLU H 158 " pdb=" N PRO H 159 " pdb=" CD PRO H 159 " ideal model delta sigma weight residual 120.60 113.12 7.48 2.20e+00 2.07e-01 1.16e+01 angle pdb=" N TYR A 144 " pdb=" CA TYR A 144 " pdb=" C TYR A 144 " ideal model delta sigma weight residual 108.46 113.39 -4.93 1.51e+00 4.39e-01 1.07e+01 angle pdb=" CA PRO H 159 " pdb=" N PRO H 159 " pdb=" CD PRO H 159 " ideal model delta sigma weight residual 111.50 107.46 4.04 1.40e+00 5.10e-01 8.34e+00 angle pdb=" CA GLU A 96 " pdb=" CB GLU A 96 " pdb=" CG GLU A 96 " ideal model delta sigma weight residual 114.10 119.83 -5.73 2.00e+00 2.50e-01 8.21e+00 angle pdb=" C GLU H 158 " pdb=" N PRO H 159 " pdb=" CA PRO H 159 " ideal model delta sigma weight residual 127.00 133.63 -6.63 2.40e+00 1.74e-01 7.62e+00 ... (remaining 7827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 3112 17.83 - 35.66: 280 35.66 - 53.49: 54 53.49 - 71.32: 8 71.32 - 89.14: 4 Dihedral angle restraints: 3458 sinusoidal: 1396 harmonic: 2062 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 36.85 56.15 1 1.00e+01 1.00e-02 4.25e+01 dihedral pdb=" CA THR A 19 " pdb=" C THR A 19 " pdb=" N THR A 20 " pdb=" CA THR A 20 " ideal model delta harmonic sigma weight residual 180.00 152.77 27.23 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA PRO A 82 " pdb=" C PRO A 82 " pdb=" N VAL A 83 " pdb=" CA VAL A 83 " ideal model delta harmonic sigma weight residual 180.00 154.13 25.87 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 3455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 839 0.106 - 0.213: 32 0.213 - 0.319: 2 0.319 - 0.425: 1 0.425 - 0.532: 1 Chirality restraints: 875 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.07e+00 chirality pdb=" CB ILE A 210 " pdb=" CA ILE A 210 " pdb=" CG1 ILE A 210 " pdb=" CG2 ILE A 210 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB ILE L 76 " pdb=" CA ILE L 76 " pdb=" CG1 ILE L 76 " pdb=" CG2 ILE L 76 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 872 not shown) Planarity restraints: 1005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 119 " -0.061 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO L 120 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO L 120 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO L 120 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 158 " -0.057 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO H 159 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 135 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO H 136 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO H 136 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 136 " -0.030 5.00e-02 4.00e+02 ... (remaining 1002 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 764 2.74 - 3.28: 6066 3.28 - 3.82: 9555 3.82 - 4.36: 11231 4.36 - 4.90: 18714 Nonbonded interactions: 46330 Sorted by model distance: nonbonded pdb=" OE2 GLU A 156 " pdb=" OH TYR A 160 " model vdw 2.203 2.440 nonbonded pdb=" OE1 GLN L 166 " pdb=" OG SER L 171 " model vdw 2.209 2.440 nonbonded pdb=" NH2 ARG A 158 " pdb=" OD1 ASP H 101 " model vdw 2.212 2.520 nonbonded pdb=" O GLN A 14 " pdb=" NH1 ARG A 158 " model vdw 2.217 2.520 nonbonded pdb=" O TYR L 186 " pdb=" OH TYR L 192 " model vdw 2.229 2.440 ... (remaining 46325 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.680 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.050 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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 : 0.006 0.061 5758 Z= 0.418 Angle : 0.825 8.203 7832 Z= 0.444 Chirality : 0.053 0.532 875 Planarity : 0.006 0.092 1000 Dihedral : 13.902 89.144 2126 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.87 % Favored : 85.13 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -2.74 (0.31), residues: 706 helix: -2.65 (1.15), residues: 14 sheet: -1.13 (0.31), residues: 269 loop : -2.35 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 258 HIS 0.003 0.001 HIS H 35 PHE 0.020 0.002 PHE L 72 TYR 0.035 0.002 TYR A 144 ARG 0.005 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 THR cc_start: 0.6470 (t) cc_final: 0.6260 (t) REVERT: A 56 LEU cc_start: 0.9064 (tp) cc_final: 0.8691 (tp) REVERT: A 100 ILE cc_start: 0.9421 (tt) cc_final: 0.9202 (tt) REVERT: H 90 ASP cc_start: 0.9094 (m-30) cc_final: 0.8846 (m-30) REVERT: H 99 ASP cc_start: 0.9256 (t0) cc_final: 0.8997 (t0) REVERT: H 104 TYR cc_start: 0.8107 (t80) cc_final: 0.7561 (t80) REVERT: L 88 TYR cc_start: 0.9417 (m-80) cc_final: 0.9138 (m-80) REVERT: L 139 PHE cc_start: 0.8581 (p90) cc_final: 0.8362 (p90) REVERT: L 142 ARG cc_start: 0.8410 (tpt90) cc_final: 0.8165 (tpt90) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1708 time to fit residues: 28.5035 Evaluate side-chains 94 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 40 optimal weight: 30.0000 chunk 63 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 ASN L 39 GLN ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5758 Z= 0.233 Angle : 0.739 9.240 7832 Z= 0.382 Chirality : 0.051 0.467 875 Planarity : 0.006 0.071 1000 Dihedral : 6.725 43.572 880 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 0.81 % Allowed : 13.45 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -2.58 (0.30), residues: 706 helix: -1.98 (1.12), residues: 14 sheet: -1.02 (0.29), residues: 276 loop : -2.27 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 258 HIS 0.005 0.001 HIS A 146 PHE 0.016 0.002 PHE L 72 TYR 0.021 0.002 TYR A 144 ARG 0.008 0.001 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9006 (tp) cc_final: 0.8592 (tp) REVERT: A 157 PHE cc_start: 0.8775 (m-80) cc_final: 0.8476 (m-10) REVERT: A 215 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8281 (p0) REVERT: H 99 ASP cc_start: 0.9129 (t0) cc_final: 0.8886 (t0) REVERT: H 104 TYR cc_start: 0.7923 (t80) cc_final: 0.7453 (t80) REVERT: H 164 TRP cc_start: 0.7995 (m100) cc_final: 0.7338 (m100) REVERT: L 90 GLN cc_start: 0.8449 (tt0) cc_final: 0.8187 (tt0) REVERT: L 139 PHE cc_start: 0.8714 (p90) cc_final: 0.8498 (p90) REVERT: L 142 ARG cc_start: 0.8389 (tpt90) cc_final: 0.8102 (tpt90) outliers start: 5 outliers final: 3 residues processed: 116 average time/residue: 0.1739 time to fit residues: 26.4032 Evaluate side-chains 99 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 0.0470 chunk 17 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5758 Z= 0.176 Angle : 0.704 9.131 7832 Z= 0.352 Chirality : 0.049 0.417 875 Planarity : 0.005 0.063 1000 Dihedral : 5.872 26.934 880 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 1.78 % Allowed : 18.96 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.30), residues: 706 helix: -1.39 (1.25), residues: 14 sheet: -0.73 (0.29), residues: 273 loop : -2.11 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 258 HIS 0.003 0.001 HIS A 146 PHE 0.026 0.002 PHE L 209 TYR 0.015 0.001 TYR L 140 ARG 0.003 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 0.690 Fit side-chains REVERT: A 56 LEU cc_start: 0.8968 (tp) cc_final: 0.8535 (tp) REVERT: A 140 PHE cc_start: 0.9595 (p90) cc_final: 0.9153 (p90) REVERT: A 156 GLU cc_start: 0.8324 (pt0) cc_final: 0.8096 (pt0) REVERT: A 157 PHE cc_start: 0.8583 (m-80) cc_final: 0.8292 (m-10) REVERT: A 202 LYS cc_start: 0.8652 (mttp) cc_final: 0.8449 (mmtp) REVERT: A 215 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8142 (p0) REVERT: A 253 ASP cc_start: 0.7057 (m-30) cc_final: 0.6713 (m-30) REVERT: H 161 THR cc_start: 0.8919 (m) cc_final: 0.8624 (p) REVERT: H 164 TRP cc_start: 0.8045 (m100) cc_final: 0.7764 (m100) REVERT: L 90 GLN cc_start: 0.8497 (tt0) cc_final: 0.8277 (tt0) REVERT: L 139 PHE cc_start: 0.8706 (p90) cc_final: 0.8462 (p90) REVERT: L 142 ARG cc_start: 0.8336 (tpt90) cc_final: 0.8020 (tpt90) outliers start: 11 outliers final: 7 residues processed: 128 average time/residue: 0.1726 time to fit residues: 28.9178 Evaluate side-chains 104 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 115 GLN H 207 ASN ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5758 Z= 0.271 Angle : 0.701 7.781 7832 Z= 0.356 Chirality : 0.048 0.420 875 Planarity : 0.005 0.063 1000 Dihedral : 5.792 25.628 880 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.46 % Favored : 87.54 % Rotamer: Outliers : 3.89 % Allowed : 18.64 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -2.21 (0.30), residues: 706 helix: -1.04 (1.35), residues: 14 sheet: -0.79 (0.29), residues: 276 loop : -2.03 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 258 HIS 0.004 0.001 HIS A 146 PHE 0.017 0.002 PHE L 72 TYR 0.024 0.002 TYR A 144 ARG 0.004 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 0.592 Fit side-chains REVERT: A 56 LEU cc_start: 0.8989 (tp) cc_final: 0.8550 (tp) REVERT: A 157 PHE cc_start: 0.8668 (m-80) cc_final: 0.8413 (m-10) REVERT: A 215 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8117 (p0) REVERT: H 99 ASP cc_start: 0.9021 (t0) cc_final: 0.8695 (t0) REVERT: L 90 GLN cc_start: 0.8560 (tt0) cc_final: 0.8257 (tt0) REVERT: L 142 ARG cc_start: 0.8307 (tpt90) cc_final: 0.7974 (tpt90) outliers start: 24 outliers final: 14 residues processed: 120 average time/residue: 0.1685 time to fit residues: 26.4543 Evaluate side-chains 109 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 206 CYS Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 27 optimal weight: 0.0670 chunk 57 optimal weight: 0.2980 chunk 46 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 60 optimal weight: 0.0070 chunk 17 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.2740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5758 Z= 0.195 Angle : 0.690 8.601 7832 Z= 0.350 Chirality : 0.048 0.402 875 Planarity : 0.005 0.061 1000 Dihedral : 5.513 24.777 880 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 3.40 % Allowed : 20.75 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.30), residues: 706 helix: -0.96 (1.41), residues: 14 sheet: -0.86 (0.29), residues: 289 loop : -1.95 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 258 HIS 0.002 0.001 HIS A 146 PHE 0.018 0.002 PHE L 72 TYR 0.023 0.001 TYR L 140 ARG 0.004 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8975 (tp) cc_final: 0.8558 (tp) REVERT: A 140 PHE cc_start: 0.9581 (p90) cc_final: 0.9110 (p90) REVERT: A 156 GLU cc_start: 0.8283 (pt0) cc_final: 0.8025 (pt0) REVERT: A 157 PHE cc_start: 0.8578 (m-80) cc_final: 0.8330 (m-10) REVERT: H 164 TRP cc_start: 0.8101 (m100) cc_final: 0.7447 (m100) REVERT: H 222 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8160 (mm-30) REVERT: L 80 GLU cc_start: 0.8201 (mp0) cc_final: 0.7843 (mp0) REVERT: L 90 GLN cc_start: 0.8558 (tt0) cc_final: 0.8233 (tt0) REVERT: L 105 GLU cc_start: 0.8656 (tt0) cc_final: 0.8223 (tm-30) REVERT: L 142 ARG cc_start: 0.8183 (tpt90) cc_final: 0.7826 (tpt90) outliers start: 21 outliers final: 16 residues processed: 133 average time/residue: 0.1589 time to fit residues: 27.8623 Evaluate side-chains 124 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 206 CYS Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.6980 chunk 67 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 5 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 7 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5758 Z= 0.171 Angle : 0.695 8.797 7832 Z= 0.350 Chirality : 0.049 0.387 875 Planarity : 0.005 0.046 1000 Dihedral : 5.270 24.293 880 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 3.08 % Allowed : 22.04 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -2.08 (0.31), residues: 706 helix: -0.98 (1.41), residues: 14 sheet: -0.79 (0.28), residues: 314 loop : -1.94 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 258 HIS 0.002 0.001 HIS H 174 PHE 0.019 0.002 PHE L 47 TYR 0.027 0.001 TYR L 140 ARG 0.002 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.647 Fit side-chains REVERT: A 56 LEU cc_start: 0.8950 (tp) cc_final: 0.8510 (tp) REVERT: A 140 PHE cc_start: 0.9533 (p90) cc_final: 0.9115 (p90) REVERT: A 156 GLU cc_start: 0.8257 (pt0) cc_final: 0.8003 (pt0) REVERT: H 161 THR cc_start: 0.8889 (m) cc_final: 0.8595 (p) REVERT: L 37 TYR cc_start: 0.9048 (m-80) cc_final: 0.8610 (m-80) REVERT: L 142 ARG cc_start: 0.8162 (tpt90) cc_final: 0.7838 (tpt90) outliers start: 19 outliers final: 17 residues processed: 131 average time/residue: 0.1747 time to fit residues: 29.7833 Evaluate side-chains 119 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 206 CYS Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 41 optimal weight: 40.0000 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5758 Z= 0.203 Angle : 0.683 8.959 7832 Z= 0.348 Chirality : 0.048 0.382 875 Planarity : 0.005 0.046 1000 Dihedral : 5.221 26.549 880 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 4.05 % Allowed : 23.01 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.31), residues: 706 helix: -1.04 (1.36), residues: 14 sheet: -0.74 (0.28), residues: 322 loop : -1.97 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 36 HIS 0.004 0.001 HIS A 146 PHE 0.019 0.002 PHE L 47 TYR 0.030 0.001 TYR L 140 ARG 0.004 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7990 (t70) cc_final: 0.7775 (t70) REVERT: A 56 LEU cc_start: 0.8972 (tp) cc_final: 0.8519 (tp) REVERT: A 140 PHE cc_start: 0.9532 (p90) cc_final: 0.9144 (p90) REVERT: A 156 GLU cc_start: 0.8146 (pt0) cc_final: 0.7854 (pt0) REVERT: H 161 THR cc_start: 0.8936 (m) cc_final: 0.8645 (p) REVERT: L 37 TYR cc_start: 0.9090 (m-80) cc_final: 0.8686 (m-80) outliers start: 25 outliers final: 20 residues processed: 129 average time/residue: 0.1706 time to fit residues: 29.2953 Evaluate side-chains 124 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 206 CYS Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.5980 chunk 42 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 61 optimal weight: 0.0470 chunk 64 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 37 optimal weight: 0.5980 overall best weight: 1.4482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 5758 Z= 0.221 Angle : 0.694 9.505 7832 Z= 0.353 Chirality : 0.048 0.382 875 Planarity : 0.005 0.046 1000 Dihedral : 5.304 30.726 880 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 3.89 % Allowed : 23.18 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.03 (0.31), residues: 706 helix: -1.06 (1.35), residues: 14 sheet: -0.68 (0.28), residues: 320 loop : -1.99 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 258 HIS 0.004 0.001 HIS A 146 PHE 0.022 0.002 PHE L 84 TYR 0.031 0.002 TYR L 140 ARG 0.004 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8979 (tp) cc_final: 0.8529 (tp) REVERT: A 140 PHE cc_start: 0.9535 (p90) cc_final: 0.9126 (p90) REVERT: A 152 TRP cc_start: 0.7160 (OUTLIER) cc_final: 0.5587 (p90) REVERT: A 156 GLU cc_start: 0.8095 (pt0) cc_final: 0.7801 (pt0) REVERT: H 155 TYR cc_start: 0.8332 (p90) cc_final: 0.8113 (p90) REVERT: H 161 THR cc_start: 0.8931 (m) cc_final: 0.8649 (p) REVERT: L 37 TYR cc_start: 0.9070 (m-80) cc_final: 0.8704 (m-80) REVERT: L 142 ARG cc_start: 0.8209 (tpt90) cc_final: 0.7797 (tpt90) REVERT: L 145 LYS cc_start: 0.9031 (mmmm) cc_final: 0.8814 (mmmm) outliers start: 24 outliers final: 18 residues processed: 127 average time/residue: 0.1638 time to fit residues: 27.3447 Evaluate side-chains 124 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 206 CYS Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 5758 Z= 0.245 Angle : 0.718 10.202 7832 Z= 0.362 Chirality : 0.049 0.386 875 Planarity : 0.005 0.049 1000 Dihedral : 5.384 28.344 880 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.47 % Favored : 88.53 % Rotamer: Outliers : 3.24 % Allowed : 23.50 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.31), residues: 706 helix: -1.08 (1.35), residues: 14 sheet: -0.74 (0.29), residues: 300 loop : -1.89 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 258 HIS 0.004 0.001 HIS A 146 PHE 0.019 0.002 PHE L 47 TYR 0.034 0.002 TYR L 140 ARG 0.004 0.001 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8103 (t70) cc_final: 0.7879 (t70) REVERT: A 56 LEU cc_start: 0.8993 (tp) cc_final: 0.8552 (tp) REVERT: A 140 PHE cc_start: 0.9559 (p90) cc_final: 0.9131 (p90) REVERT: A 152 TRP cc_start: 0.7221 (OUTLIER) cc_final: 0.5778 (p90) REVERT: A 156 GLU cc_start: 0.8189 (pt0) cc_final: 0.7913 (pt0) REVERT: H 161 THR cc_start: 0.8940 (m) cc_final: 0.8650 (p) REVERT: L 37 TYR cc_start: 0.9108 (m-80) cc_final: 0.8710 (m-80) REVERT: L 142 ARG cc_start: 0.8194 (tpt90) cc_final: 0.7770 (tpt90) REVERT: L 145 LYS cc_start: 0.9018 (mmmm) cc_final: 0.8806 (mmmm) outliers start: 20 outliers final: 17 residues processed: 120 average time/residue: 0.1671 time to fit residues: 26.2596 Evaluate side-chains 117 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 206 CYS Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5758 Z= 0.197 Angle : 0.718 10.670 7832 Z= 0.358 Chirality : 0.049 0.377 875 Planarity : 0.005 0.050 1000 Dihedral : 5.271 26.917 880 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 2.92 % Allowed : 24.15 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -2.06 (0.31), residues: 706 helix: -0.97 (1.36), residues: 14 sheet: -0.74 (0.29), residues: 303 loop : -1.94 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 258 HIS 0.003 0.001 HIS A 146 PHE 0.026 0.002 PHE L 72 TYR 0.033 0.002 TYR L 140 ARG 0.003 0.000 ARG H 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7551 (pmt-80) cc_final: 0.7259 (tpt90) REVERT: A 56 LEU cc_start: 0.8942 (tp) cc_final: 0.8527 (tp) REVERT: A 140 PHE cc_start: 0.9524 (p90) cc_final: 0.9130 (p90) REVERT: A 156 GLU cc_start: 0.8075 (pt0) cc_final: 0.7788 (pt0) REVERT: H 161 THR cc_start: 0.8935 (m) cc_final: 0.8649 (p) REVERT: L 37 TYR cc_start: 0.9094 (m-80) cc_final: 0.8690 (m-80) REVERT: L 142 ARG cc_start: 0.8185 (tpt90) cc_final: 0.7766 (tpt90) REVERT: L 145 LYS cc_start: 0.9029 (mmmm) cc_final: 0.8822 (mmmm) outliers start: 18 outliers final: 18 residues processed: 124 average time/residue: 0.1624 time to fit residues: 26.4344 Evaluate side-chains 126 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 206 CYS Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.105967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.077055 restraints weight = 13901.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.080168 restraints weight = 6921.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.082181 restraints weight = 4448.155| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 5758 Z= 0.296 Angle : 0.732 11.176 7832 Z= 0.368 Chirality : 0.050 0.386 875 Planarity : 0.005 0.051 1000 Dihedral : 5.415 25.555 880 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 3.08 % Allowed : 24.31 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.31), residues: 706 helix: -1.10 (1.32), residues: 14 sheet: -0.77 (0.29), residues: 301 loop : -1.90 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 258 HIS 0.005 0.001 HIS A 146 PHE 0.023 0.002 PHE L 72 TYR 0.028 0.002 TYR L 140 ARG 0.004 0.001 ARG L 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1489.41 seconds wall clock time: 27 minutes 50.13 seconds (1670.13 seconds total)