Starting phenix.real_space_refine on Tue Feb 11 14:54:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p8v_13255/02_2025/7p8v_13255.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p8v_13255/02_2025/7p8v_13255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p8v_13255/02_2025/7p8v_13255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p8v_13255/02_2025/7p8v_13255.map" model { file = "/net/cci-nas-00/data/ceres_data/7p8v_13255/02_2025/7p8v_13255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p8v_13255/02_2025/7p8v_13255.cif" } resolution = 3.6 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= 0.001 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: 6 Type Number sf(0) Gaussians P 41 5.49 5 Mg 2 5.21 5 S 16 5.16 5 C 3625 2.51 5 N 1108 2.21 5 O 1196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5988 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2601 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 13, 'TRANS': 317} Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2601 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 13, 'TRANS': 317} Chain: "C" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 458 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.39, per 1000 atoms: 0.73 Number of scatterers: 5988 At special positions: 0 Unit cell: (81.605, 73.015, 109.093, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 16 16.00 P 41 15.00 Mg 2 11.99 O 1196 8.00 N 1108 7.00 C 3625 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: 1.52 Conformation dependent library (CDL) restraints added in 799.3 milliseconds 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1244 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 9 sheets defined 39.9% alpha, 21.1% beta 12 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 7 through 20 removed outlier: 3.748A pdb=" N GLU A 18 " --> pdb=" O ILE A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 38 Processing helix chain 'A' and resid 64 through 72 removed outlier: 3.754A pdb=" N LEU A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 96 through 105 removed outlier: 4.126A pdb=" N ALA A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.620A pdb=" N LYS A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 182 removed outlier: 4.029A pdb=" N GLU A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 223 removed outlier: 7.471A pdb=" N THR A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N ALA A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 314 through 330 Processing helix chain 'B' and resid 7 through 20 removed outlier: 3.780A pdb=" N GLU B 18 " --> pdb=" O ILE B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 Processing helix chain 'B' and resid 64 through 73 removed outlier: 4.151A pdb=" N ALA B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 98 through 105 removed outlier: 3.632A pdb=" N ILE B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 163 through 182 Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.514A pdb=" N LEU B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 223 Processing helix chain 'B' and resid 265 through 279 Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 314 through 330 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 137 removed outlier: 3.726A pdb=" N ALA A 120 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA A 125 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU A 108 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 148 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 146 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N HIS A 191 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE A 195 " --> pdb=" O HIS A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 77 Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 231 removed outlier: 3.671A pdb=" N GLY A 238 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR A 255 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU A 292 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N TYR A 257 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 113 removed outlier: 3.633A pdb=" N ARG B 55 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 197 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N HIS B 191 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE B 195 " --> pdb=" O HIS B 191 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 126 removed outlier: 3.644A pdb=" N ALA B 120 " --> pdb=" O ALA B 137 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 224 through 230 removed outlier: 3.714A pdb=" N GLY B 238 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TYR B 255 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N LEU B 292 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR B 257 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N CYS B 256 " --> pdb=" O MET B 263 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 299 through 300 262 hydrogen bonds defined for protein. 747 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 951 1.31 - 1.44: 1701 1.44 - 1.56: 3415 1.56 - 1.69: 78 1.69 - 1.82: 24 Bond restraints: 6169 Sorted by residual: bond pdb=" N3B ANP A 701 " pdb=" PG ANP A 701 " ideal model delta sigma weight residual 1.795 1.620 0.175 2.00e-02 2.50e+03 7.66e+01 bond pdb=" N3B ANP B 702 " pdb=" PG ANP B 702 " ideal model delta sigma weight residual 1.795 1.620 0.175 2.00e-02 2.50e+03 7.64e+01 bond pdb=" O3A ANP B 702 " pdb=" PB ANP B 702 " ideal model delta sigma weight residual 1.700 1.579 0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" O3A ANP A 701 " pdb=" PB ANP A 701 " ideal model delta sigma weight residual 1.700 1.589 0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" O3G ANP A 701 " pdb=" PG ANP A 701 " ideal model delta sigma weight residual 1.528 1.424 0.104 2.00e-02 2.50e+03 2.73e+01 ... (remaining 6164 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 7056 2.56 - 5.12: 1429 5.12 - 7.68: 34 7.68 - 10.24: 3 10.24 - 12.80: 3 Bond angle restraints: 8525 Sorted by residual: angle pdb=" CA GLY B 127 " pdb=" C GLY B 127 " pdb=" O GLY B 127 " ideal model delta sigma weight residual 122.52 117.40 5.12 7.90e-01 1.60e+00 4.19e+01 angle pdb=" C GLN A 117 " pdb=" CA GLN A 117 " pdb=" CB GLN A 117 " ideal model delta sigma weight residual 109.54 120.67 -11.13 1.84e+00 2.95e-01 3.66e+01 angle pdb=" CA GLY A 127 " pdb=" C GLY A 127 " pdb=" O GLY A 127 " ideal model delta sigma weight residual 122.52 118.13 4.39 7.90e-01 1.60e+00 3.09e+01 angle pdb=" CA GLY A 217 " pdb=" C GLY A 217 " pdb=" O GLY A 217 " ideal model delta sigma weight residual 122.39 117.41 4.98 9.30e-01 1.16e+00 2.87e+01 angle pdb=" CA PRO A 7 " pdb=" C PRO A 7 " pdb=" O PRO A 7 " ideal model delta sigma weight residual 120.90 117.14 3.76 7.20e-01 1.93e+00 2.73e+01 ... (remaining 8520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.54: 3336 29.54 - 59.07: 312 59.07 - 88.60: 19 88.60 - 118.14: 1 118.14 - 147.67: 2 Dihedral angle restraints: 3670 sinusoidal: 1752 harmonic: 1918 Sorted by residual: dihedral pdb=" C GLN A 117 " pdb=" N GLN A 117 " pdb=" CA GLN A 117 " pdb=" CB GLN A 117 " ideal model delta harmonic sigma weight residual -122.60 -134.60 12.00 0 2.50e+00 1.60e-01 2.30e+01 dihedral pdb=" O1B ANP A 701 " pdb=" N3B ANP A 701 " pdb=" PB ANP A 701 " pdb=" PG ANP A 701 " ideal model delta sinusoidal sigma weight residual 35.15 -177.18 -147.67 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" O1A ANP B 702 " pdb=" O3A ANP B 702 " pdb=" PA ANP B 702 " pdb=" PB ANP B 702 " ideal model delta sinusoidal sigma weight residual 83.11 -46.03 129.14 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 3667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 354 0.061 - 0.121: 368 0.121 - 0.182: 186 0.182 - 0.242: 52 0.242 - 0.303: 6 Chirality restraints: 966 Sorted by residual: chirality pdb=" CA GLN A 117 " pdb=" N GLN A 117 " pdb=" C GLN A 117 " pdb=" CB GLN A 117 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA LEU B 234 " pdb=" N LEU B 234 " pdb=" C LEU B 234 " pdb=" CB LEU B 234 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C3' ANP A 701 " pdb=" C2' ANP A 701 " pdb=" C4' ANP A 701 " pdb=" O3' ANP A 701 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 963 not shown) Planarity restraints: 983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 208 " -0.019 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C LYS A 208 " 0.068 2.00e-02 2.50e+03 pdb=" O LYS A 208 " -0.025 2.00e-02 2.50e+03 pdb=" N GLU A 209 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 163 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C THR A 163 " 0.055 2.00e-02 2.50e+03 pdb=" O THR A 163 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 164 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 185 " 0.014 2.00e-02 2.50e+03 2.93e-02 8.56e+00 pdb=" C VAL B 185 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL B 185 " 0.019 2.00e-02 2.50e+03 pdb=" N THR B 186 " 0.018 2.00e-02 2.50e+03 ... (remaining 980 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 829 2.81 - 3.33: 5816 3.33 - 3.85: 9502 3.85 - 4.38: 12614 4.38 - 4.90: 19284 Nonbonded interactions: 48045 Sorted by model distance: nonbonded pdb=" OD1 ASN A 33 " pdb="MG MG A 702 " model vdw 2.287 2.170 nonbonded pdb="MG MG B 701 " pdb=" O2B ANP B 702 " model vdw 2.320 2.170 nonbonded pdb=" OD1 ASN B 33 " pdb="MG MG B 701 " model vdw 2.337 2.170 nonbonded pdb=" O3G ANP A 701 " pdb="MG MG A 702 " model vdw 2.341 2.170 nonbonded pdb=" O1A ANP A 701 " pdb="MG MG A 702 " model vdw 2.374 2.170 ... (remaining 48040 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 331) selection = (chain 'B' and resid 1 through 331) } 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.250 Find NCS groups from input model: 0.220 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 : 0.013 0.175 6169 Z= 0.866 Angle : 1.812 12.797 8525 Z= 1.349 Chirality : 0.102 0.303 966 Planarity : 0.009 0.040 983 Dihedral : 20.306 147.672 2426 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.36 % Allowed : 7.85 % Favored : 91.79 % Cbeta Deviations : 0.16 % 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: -0.42 (0.31), residues: 658 helix: 1.02 (0.32), residues: 250 sheet: -0.83 (0.39), residues: 150 loop : -1.15 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP A 229 HIS 0.011 0.003 HIS B 170 PHE 0.031 0.005 PHE A 168 TYR 0.017 0.004 TYR A 257 ARG 0.013 0.002 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 143 THR cc_start: 0.9100 (m) cc_final: 0.8816 (p) REVERT: A 169 ASN cc_start: 0.8237 (m110) cc_final: 0.7878 (m110) REVERT: A 173 GLU cc_start: 0.7886 (tp30) cc_final: 0.7613 (tp30) REVERT: A 229 TRP cc_start: 0.8208 (t-100) cc_final: 0.7829 (t-100) REVERT: A 231 HIS cc_start: 0.6665 (t70) cc_final: 0.6349 (t70) REVERT: B 22 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7729 (mtm-85) REVERT: B 274 GLN cc_start: 0.7801 (mt0) cc_final: 0.7304 (tt0) outliers start: 2 outliers final: 0 residues processed: 78 average time/residue: 0.2097 time to fit residues: 21.0993 Evaluate side-chains 51 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 188 ASN B 122 GLN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.129174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.102198 restraints weight = 9410.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.104462 restraints weight = 5688.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.105349 restraints weight = 3921.496| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6169 Z= 0.224 Angle : 0.596 7.336 8525 Z= 0.326 Chirality : 0.043 0.158 966 Planarity : 0.005 0.045 983 Dihedral : 21.062 142.534 1176 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.82 % Allowed : 12.96 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.33), residues: 658 helix: 1.22 (0.32), residues: 256 sheet: -0.56 (0.39), residues: 172 loop : -0.85 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 229 HIS 0.004 0.001 HIS B 170 PHE 0.015 0.002 PHE A 183 TYR 0.010 0.002 TYR B 124 ARG 0.005 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.605 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.1654 time to fit residues: 15.6372 Evaluate side-chains 46 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 143 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.127125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.100519 restraints weight = 9714.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.102765 restraints weight = 6142.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.103387 restraints weight = 3993.945| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6169 Z= 0.230 Angle : 0.550 6.254 8525 Z= 0.302 Chirality : 0.042 0.149 966 Planarity : 0.004 0.040 983 Dihedral : 20.778 137.659 1172 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.55 % Allowed : 15.69 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.33), residues: 658 helix: 0.82 (0.32), residues: 272 sheet: -0.41 (0.40), residues: 158 loop : -1.18 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.008 0.001 HIS B 308 PHE 0.018 0.002 PHE A 168 TYR 0.009 0.001 TYR B 323 ARG 0.005 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7749 (tp30) cc_final: 0.7474 (tp30) outliers start: 14 outliers final: 8 residues processed: 57 average time/residue: 0.1830 time to fit residues: 14.3099 Evaluate side-chains 52 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.127432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.100355 restraints weight = 9771.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.103108 restraints weight = 5559.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.104957 restraints weight = 3841.240| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6169 Z= 0.213 Angle : 0.520 6.249 8525 Z= 0.282 Chirality : 0.041 0.147 966 Planarity : 0.004 0.040 983 Dihedral : 20.618 140.356 1172 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.92 % Allowed : 16.97 % Favored : 80.11 % 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: -0.22 (0.33), residues: 658 helix: 0.87 (0.33), residues: 272 sheet: -0.37 (0.41), residues: 158 loop : -1.09 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.005 0.001 HIS B 308 PHE 0.016 0.002 PHE A 168 TYR 0.009 0.001 TYR B 257 ARG 0.003 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7634 (tp30) cc_final: 0.7330 (tp30) REVERT: B 262 MET cc_start: 0.7881 (mtm) cc_final: 0.7611 (mtp) outliers start: 16 outliers final: 13 residues processed: 59 average time/residue: 0.1637 time to fit residues: 13.3473 Evaluate side-chains 54 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.127711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.101438 restraints weight = 9615.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.102578 restraints weight = 6249.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104719 restraints weight = 4450.640| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6169 Z= 0.199 Angle : 0.513 6.693 8525 Z= 0.276 Chirality : 0.041 0.146 966 Planarity : 0.004 0.040 983 Dihedral : 20.512 141.810 1172 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.20 % Allowed : 16.24 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.34), residues: 658 helix: 0.86 (0.33), residues: 272 sheet: -0.55 (0.41), residues: 164 loop : -0.95 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 229 HIS 0.003 0.001 HIS B 308 PHE 0.015 0.002 PHE A 168 TYR 0.009 0.001 TYR B 257 ARG 0.003 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7546 (tp30) cc_final: 0.7243 (tp30) REVERT: B 262 MET cc_start: 0.7866 (mtm) cc_final: 0.7624 (mtp) outliers start: 23 outliers final: 14 residues processed: 63 average time/residue: 0.1902 time to fit residues: 16.0764 Evaluate side-chains 51 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 41 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.126717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.100475 restraints weight = 9570.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.102924 restraints weight = 6066.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.103474 restraints weight = 4009.926| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6169 Z= 0.236 Angle : 0.522 6.546 8525 Z= 0.281 Chirality : 0.041 0.148 966 Planarity : 0.004 0.040 983 Dihedral : 20.432 143.127 1172 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.74 % Allowed : 18.61 % Favored : 78.65 % 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: -0.26 (0.34), residues: 658 helix: 0.85 (0.33), residues: 272 sheet: -0.59 (0.41), residues: 168 loop : -0.96 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS B 304 PHE 0.018 0.002 PHE A 168 TYR 0.009 0.001 TYR B 257 ARG 0.003 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7594 (tp30) cc_final: 0.7231 (tp30) REVERT: B 262 MET cc_start: 0.7856 (mtm) cc_final: 0.7601 (mtp) outliers start: 15 outliers final: 14 residues processed: 50 average time/residue: 0.1591 time to fit residues: 11.4691 Evaluate side-chains 50 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 36 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.121139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.091905 restraints weight = 9975.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.095050 restraints weight = 5211.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.097254 restraints weight = 3429.511| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6169 Z= 0.189 Angle : 0.490 6.235 8525 Z= 0.265 Chirality : 0.040 0.143 966 Planarity : 0.004 0.042 983 Dihedral : 20.271 146.382 1172 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.65 % Allowed : 17.52 % Favored : 78.83 % 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: -0.12 (0.34), residues: 658 helix: 0.90 (0.33), residues: 272 sheet: -0.42 (0.42), residues: 164 loop : -0.88 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.004 0.001 HIS A 308 PHE 0.011 0.002 PHE B 168 TYR 0.009 0.001 TYR B 257 ARG 0.003 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 162 ARG cc_start: 0.8203 (mmp-170) cc_final: 0.7949 (mmp-170) REVERT: A 173 GLU cc_start: 0.7566 (tp30) cc_final: 0.7242 (tp30) REVERT: B 262 MET cc_start: 0.7942 (mtm) cc_final: 0.7674 (mtp) outliers start: 20 outliers final: 15 residues processed: 58 average time/residue: 0.1827 time to fit residues: 14.6683 Evaluate side-chains 50 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.118943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.089869 restraints weight = 9953.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.093040 restraints weight = 5202.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.095222 restraints weight = 3412.717| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6169 Z= 0.260 Angle : 0.536 6.549 8525 Z= 0.287 Chirality : 0.041 0.161 966 Planarity : 0.004 0.041 983 Dihedral : 20.308 148.505 1172 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.65 % Allowed : 18.43 % Favored : 77.92 % 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: -0.24 (0.34), residues: 658 helix: 0.84 (0.33), residues: 272 sheet: -0.55 (0.40), residues: 168 loop : -0.93 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 229 HIS 0.006 0.001 HIS B 308 PHE 0.021 0.002 PHE A 168 TYR 0.010 0.001 TYR B 257 ARG 0.002 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 162 ARG cc_start: 0.8207 (mmp-170) cc_final: 0.7997 (mmp-170) REVERT: A 173 GLU cc_start: 0.7759 (tp30) cc_final: 0.7389 (tp30) REVERT: B 262 MET cc_start: 0.7919 (mtm) cc_final: 0.7597 (mtp) outliers start: 20 outliers final: 16 residues processed: 57 average time/residue: 0.1469 time to fit residues: 12.1543 Evaluate side-chains 52 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.118121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.087932 restraints weight = 10358.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.091046 restraints weight = 5584.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.093139 restraints weight = 3750.889| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6169 Z= 0.350 Angle : 0.587 6.551 8525 Z= 0.315 Chirality : 0.043 0.155 966 Planarity : 0.004 0.042 983 Dihedral : 20.348 150.246 1172 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.28 % Allowed : 18.80 % Favored : 77.92 % 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: -0.38 (0.34), residues: 658 helix: 0.74 (0.33), residues: 270 sheet: -0.61 (0.40), residues: 168 loop : -1.04 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 229 HIS 0.005 0.001 HIS B 75 PHE 0.025 0.003 PHE A 168 TYR 0.014 0.002 TYR B 291 ARG 0.003 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.641 Fit side-chains REVERT: A 173 GLU cc_start: 0.7752 (tp30) cc_final: 0.7265 (tp30) outliers start: 18 outliers final: 16 residues processed: 53 average time/residue: 0.1870 time to fit residues: 14.0354 Evaluate side-chains 52 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.119910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.089913 restraints weight = 10156.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.092986 restraints weight = 5516.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.095081 restraints weight = 3729.182| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6169 Z= 0.230 Angle : 0.535 7.012 8525 Z= 0.287 Chirality : 0.041 0.151 966 Planarity : 0.004 0.078 983 Dihedral : 20.234 149.315 1172 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.47 % Allowed : 18.25 % Favored : 78.28 % 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: -0.34 (0.34), residues: 658 helix: 0.75 (0.33), residues: 272 sheet: -0.59 (0.40), residues: 168 loop : -0.99 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 229 HIS 0.003 0.001 HIS A 308 PHE 0.018 0.002 PHE A 168 TYR 0.010 0.001 TYR B 257 ARG 0.007 0.000 ARG A 162 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 36 time to evaluate : 0.633 Fit side-chains REVERT: A 173 GLU cc_start: 0.7680 (tp30) cc_final: 0.7231 (tp30) outliers start: 19 outliers final: 17 residues processed: 50 average time/residue: 0.1471 time to fit residues: 10.6638 Evaluate side-chains 51 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 34 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 61 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.120107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.089830 restraints weight = 10277.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.092983 restraints weight = 5487.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.095111 restraints weight = 3676.732| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6169 Z= 0.231 Angle : 0.537 9.047 8525 Z= 0.288 Chirality : 0.041 0.149 966 Planarity : 0.004 0.044 983 Dihedral : 20.132 149.711 1172 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.28 % Allowed : 18.61 % Favored : 78.10 % 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: -0.33 (0.34), residues: 658 helix: 0.78 (0.33), residues: 272 sheet: -0.57 (0.40), residues: 168 loop : -1.05 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 229 HIS 0.009 0.001 HIS B 245 PHE 0.018 0.002 PHE A 168 TYR 0.010 0.001 TYR B 257 ARG 0.008 0.000 ARG A 162 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1807.85 seconds wall clock time: 33 minutes 16.97 seconds (1996.97 seconds total)