Starting phenix.real_space_refine on Thu Jul 2 02:46:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7p8v_13255/07_2026/7p8v_13255.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p8v_13255/07_2026/7p8v_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_13255/07_2026/7p8v_13255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p8v_13255/07_2026/7p8v_13255.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7p8v_13255/07_2026/7p8v_13255.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7p8v_13255/07_2026/7p8v_13255.cif" model { file = "/net/cci-nas-00/data/ceres_data/7p8v_13255/07_2026/7p8v_13255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p8v_13255/07_2026/7p8v_13255.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 1.65, per 1000 atoms: 0.28 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: 0.54 Conformation dependent library (CDL) restraints added in 194.0 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: 0.70 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: 1.08 Time building geometry restraints manager: 0.72 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: 7069 2.56 - 5.12: 1416 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: 3296 29.54 - 59.07: 298 59.07 - 88.60: 17 88.60 - 118.14: 1 118.14 - 147.67: 2 Dihedral angle restraints: 3614 sinusoidal: 1696 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 3611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 356 0.061 - 0.121: 379 0.121 - 0.182: 172 0.182 - 0.242: 52 0.242 - 0.303: 7 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.320 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 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= 0.990 Angle : 1.799 12.797 8525 Z= 1.347 Chirality : 0.102 0.303 966 Planarity : 0.009 0.040 983 Dihedral : 20.081 147.672 2370 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.013 0.002 ARG B 211 TYR 0.017 0.004 TYR A 257 PHE 0.031 0.005 PHE A 168 TRP 0.018 0.004 TRP A 229 HIS 0.011 0.003 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.01348 / 0.99 ( 6169) covalent geometry : angle 1.79941 / 1.35 ( 8525) hydrogen bonds : bond 0.21398 / 15.03 ( 291) hydrogen bonds : angle 8.14779 / 5.92 ( 805) *********************** 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 : 0.140 Fit side-chains revert: symmetry clash REVERT: A 143 THR cc_start: 0.9100 (m) cc_final: 0.8815 (p) REVERT: A 169 ASN cc_start: 0.8238 (m110) cc_final: 0.7879 (m110) REVERT: A 173 GLU cc_start: 0.7886 (tp30) cc_final: 0.7614 (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: 0.6350 (t70) REVERT: B 22 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7728 (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: 0.0796 time to fit residues: 8.0579 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 : 0.203 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.0470 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 GLN A 188 ASN A 308 HIS B 122 GLN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.129260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.102046 restraints weight = 9435.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.104483 restraints weight = 5648.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.105182 restraints weight = 3856.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.105699 restraints weight = 3307.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105831 restraints weight = 3149.421| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6169 Z= 0.157 Angle : 0.663 7.342 8525 Z= 0.357 Chirality : 0.047 0.164 966 Planarity : 0.005 0.041 983 Dihedral : 21.520 142.219 1120 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.64 % Allowed : 13.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.32), residues: 658 helix: 0.75 (0.31), residues: 268 sheet: -0.64 (0.40), residues: 160 loop : -1.36 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 113 TYR 0.012 0.002 TYR B 124 PHE 0.022 0.002 PHE A 168 TRP 0.013 0.001 TRP A 229 HIS 0.004 0.001 HIS B 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 ( 6169) covalent geometry : angle 0.66271 / 0.36 ( 8525) hydrogen bonds : bond 0.05326 / 3.66 ( 291) hydrogen bonds : angle 5.88923 / 4.19 ( 805) *********************** 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 61 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.211 Fit side-chains REVERT: B 153 ASN cc_start: 0.7652 (t0) cc_final: 0.7443 (t0) outliers start: 9 outliers final: 6 residues processed: 60 average time/residue: 0.0655 time to fit residues: 5.5773 Evaluate side-chains 45 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 B residue 27 VAL Chi-restraints excluded: chain B residue 94 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 0.0570 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.128037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.101381 restraints weight = 9479.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102976 restraints weight = 6049.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.104056 restraints weight = 4067.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104308 restraints weight = 3552.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.105450 restraints weight = 3311.206| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6169 Z= 0.144 Angle : 0.571 6.625 8525 Z= 0.308 Chirality : 0.044 0.149 966 Planarity : 0.004 0.040 983 Dihedral : 21.252 142.093 1116 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.37 % Allowed : 16.06 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.32), residues: 658 helix: 0.79 (0.32), residues: 270 sheet: -0.53 (0.40), residues: 160 loop : -1.31 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 95 TYR 0.009 0.001 TYR B 323 PHE 0.019 0.002 PHE A 168 TRP 0.012 0.001 TRP A 229 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 6169) covalent geometry : angle 0.57134 / 0.31 ( 8525) hydrogen bonds : bond 0.04406 / 3.11 ( 291) hydrogen bonds : angle 5.43561 / 3.83 ( 805) *********************** 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 62 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.207 Fit side-chains REVERT: A 173 GLU cc_start: 0.7579 (tp30) cc_final: 0.7254 (tp30) outliers start: 13 outliers final: 10 residues processed: 58 average time/residue: 0.0740 time to fit residues: 5.6929 Evaluate side-chains 51 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 66 ASP 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 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 323 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.0170 chunk 44 optimal weight: 5.9990 chunk 43 optimal weight: 0.1980 chunk 58 optimal weight: 0.6980 chunk 13 optimal weight: 10.0000 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 245 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.128498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.101844 restraints weight = 9541.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.103998 restraints weight = 5696.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.104781 restraints weight = 3857.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.105281 restraints weight = 3606.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.106269 restraints weight = 3141.665| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6169 Z= 0.127 Angle : 0.541 6.727 8525 Z= 0.290 Chirality : 0.043 0.146 966 Planarity : 0.004 0.049 983 Dihedral : 21.146 140.413 1116 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.10 % Allowed : 16.06 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.33), residues: 658 helix: 0.83 (0.32), residues: 270 sheet: -0.48 (0.40), residues: 160 loop : -1.21 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.008 0.001 TYR B 257 PHE 0.017 0.002 PHE A 168 TRP 0.009 0.001 TRP A 229 HIS 0.004 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 6169) covalent geometry : angle 0.54126 / 0.29 ( 8525) hydrogen bonds : bond 0.03886 / 2.73 ( 291) hydrogen bonds : angle 5.21194 / 3.66 ( 805) *********************** 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 65 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.202 Fit side-chains REVERT: A 173 GLU cc_start: 0.7525 (tp30) cc_final: 0.7194 (tp30) outliers start: 17 outliers final: 15 residues processed: 57 average time/residue: 0.0739 time to fit residues: 5.8481 Evaluate side-chains 55 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 66 ASP 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 143 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 130 MET 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 11 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.128151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.101221 restraints weight = 9727.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.102368 restraints weight = 6340.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.103595 restraints weight = 4687.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.104451 restraints weight = 3782.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104554 restraints weight = 3440.498| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6169 Z= 0.128 Angle : 0.531 6.487 8525 Z= 0.284 Chirality : 0.042 0.146 966 Planarity : 0.004 0.040 983 Dihedral : 21.048 139.907 1116 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.74 % Allowed : 17.88 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.33), residues: 658 helix: 0.78 (0.32), residues: 272 sheet: -0.47 (0.41), residues: 158 loop : -1.21 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 95 TYR 0.007 0.001 TYR B 291 PHE 0.016 0.002 PHE A 168 TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS B 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 6169) covalent geometry : angle 0.53086 / 0.28 ( 8525) hydrogen bonds : bond 0.03755 / 2.65 ( 291) hydrogen bonds : angle 5.17802 / 3.67 ( 805) *********************** 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 60 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.202 Fit side-chains REVERT: A 173 GLU cc_start: 0.7497 (tp30) cc_final: 0.7160 (tp30) REVERT: A 274 GLN cc_start: 0.8155 (mm110) cc_final: 0.7923 (mm110) outliers start: 15 outliers final: 11 residues processed: 53 average time/residue: 0.0618 time to fit residues: 4.5727 Evaluate side-chains 53 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 94 PHE 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 262 MET Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 130 MET 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: 4.9990 chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.127799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100934 restraints weight = 9643.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.103672 restraints weight = 5985.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.104133 restraints weight = 3826.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.104796 restraints weight = 3549.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.104982 restraints weight = 3128.965| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6169 Z= 0.128 Angle : 0.526 6.507 8525 Z= 0.280 Chirality : 0.042 0.147 966 Planarity : 0.004 0.040 983 Dihedral : 20.915 138.773 1116 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.38 % Allowed : 16.61 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.33), residues: 658 helix: 0.81 (0.32), residues: 272 sheet: -0.46 (0.41), residues: 158 loop : -1.14 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 95 TYR 0.007 0.001 TYR B 257 PHE 0.016 0.002 PHE A 168 TRP 0.008 0.001 TRP A 229 HIS 0.005 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 6169) covalent geometry : angle 0.52639 / 0.28 ( 8525) hydrogen bonds : bond 0.03644 / 2.57 ( 291) hydrogen bonds : angle 5.08802 / 3.62 ( 805) *********************** 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 69 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 0.197 Fit side-chains REVERT: A 173 GLU cc_start: 0.7471 (tp30) cc_final: 0.7128 (tp30) REVERT: A 274 GLN cc_start: 0.8134 (mm110) cc_final: 0.7900 (mm110) outliers start: 24 outliers final: 19 residues processed: 57 average time/residue: 0.0697 time to fit residues: 5.4722 Evaluate side-chains 57 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 66 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 143 THR Chi-restraints excluded: chain A residue 235 THR 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 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 130 MET 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 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3733 r_free = 0.3733 target = 0.127592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.100785 restraints weight = 9640.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.102855 restraints weight = 6029.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.103697 restraints weight = 4135.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.104374 restraints weight = 3853.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.104623 restraints weight = 3317.120| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6169 Z= 0.126 Angle : 0.521 6.932 8525 Z= 0.277 Chirality : 0.042 0.146 966 Planarity : 0.004 0.040 983 Dihedral : 20.803 138.985 1116 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.74 % Allowed : 17.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.34), residues: 658 helix: 0.83 (0.33), residues: 272 sheet: -0.39 (0.42), residues: 158 loop : -1.21 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 95 TYR 0.009 0.001 TYR B 257 PHE 0.016 0.002 PHE A 168 TRP 0.008 0.001 TRP A 229 HIS 0.004 0.001 HIS B 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 6169) covalent geometry : angle 0.52127 / 0.28 ( 8525) hydrogen bonds : bond 0.03573 / 2.52 ( 291) hydrogen bonds : angle 5.03826 / 3.60 ( 805) *********************** 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 69 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 43 time to evaluate : 0.230 Fit side-chains REVERT: A 173 GLU cc_start: 0.7446 (tp30) cc_final: 0.7092 (tp30) REVERT: A 274 GLN cc_start: 0.8103 (mm110) cc_final: 0.7901 (mm110) outliers start: 26 outliers final: 16 residues processed: 59 average time/residue: 0.0693 time to fit residues: 5.7376 Evaluate side-chains 56 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 235 THR 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 B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 130 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 40 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 45 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 chunk 66 optimal weight: 20.0000 chunk 12 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.126968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.099963 restraints weight = 9663.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.102672 restraints weight = 5539.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.104474 restraints weight = 3872.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.105695 restraints weight = 3068.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.106282 restraints weight = 2633.022| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6169 Z= 0.132 Angle : 0.515 6.590 8525 Z= 0.275 Chirality : 0.042 0.147 966 Planarity : 0.004 0.040 983 Dihedral : 20.735 140.286 1116 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.65 % Allowed : 18.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.34), residues: 658 helix: 0.82 (0.33), residues: 272 sheet: -0.53 (0.41), residues: 164 loop : -1.09 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 162 TYR 0.008 0.001 TYR B 257 PHE 0.017 0.002 PHE A 168 TRP 0.008 0.001 TRP B 229 HIS 0.003 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 6169) covalent geometry : angle 0.51516 / 0.27 ( 8525) hydrogen bonds : bond 0.03632 / 2.55 ( 291) hydrogen bonds : angle 5.03846 / 3.61 ( 805) *********************** 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 60 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 40 time to evaluate : 0.202 Fit side-chains REVERT: A 173 GLU cc_start: 0.7451 (tp30) cc_final: 0.7087 (tp30) outliers start: 20 outliers final: 18 residues processed: 53 average time/residue: 0.0729 time to fit residues: 5.3575 Evaluate side-chains 56 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 66 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 143 THR Chi-restraints excluded: chain A residue 235 THR 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 B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 130 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 chunk 21 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.126670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.099373 restraints weight = 9686.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.102133 restraints weight = 5603.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.103794 restraints weight = 3905.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.105105 restraints weight = 3115.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.105948 restraints weight = 2673.397| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 6169 Z= 0.130 Angle : 0.516 7.920 8525 Z= 0.276 Chirality : 0.042 0.145 966 Planarity : 0.003 0.040 983 Dihedral : 20.643 141.320 1116 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.28 % Allowed : 18.98 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.34), residues: 658 helix: 0.83 (0.33), residues: 272 sheet: -0.62 (0.41), residues: 168 loop : -1.12 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 162 TYR 0.008 0.001 TYR B 257 PHE 0.016 0.002 PHE A 168 TRP 0.008 0.001 TRP A 229 HIS 0.003 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 6169) covalent geometry : angle 0.51616 / 0.28 ( 8525) hydrogen bonds : bond 0.03593 / 2.51 ( 291) hydrogen bonds : angle 5.00819 / 3.58 ( 805) *********************** 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 59 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.208 Fit side-chains REVERT: A 173 GLU cc_start: 0.7424 (tp30) cc_final: 0.7061 (tp30) outliers start: 18 outliers final: 16 residues processed: 52 average time/residue: 0.0572 time to fit residues: 4.3598 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 : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 66 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 143 THR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 130 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 57 optimal weight: 0.3980 chunk 2 optimal weight: 0.4980 chunk 15 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.126960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.099841 restraints weight = 9700.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.102587 restraints weight = 5628.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.104467 restraints weight = 3930.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.105386 restraints weight = 3095.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.106223 restraints weight = 2709.215| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6169 Z= 0.130 Angle : 0.510 6.621 8525 Z= 0.274 Chirality : 0.041 0.146 966 Planarity : 0.004 0.040 983 Dihedral : 20.597 142.361 1116 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.28 % Allowed : 19.16 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.34), residues: 658 helix: 0.83 (0.32), residues: 272 sheet: -0.61 (0.41), residues: 168 loop : -1.06 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 264 TYR 0.008 0.001 TYR B 257 PHE 0.016 0.002 PHE A 168 TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 6169) covalent geometry : angle 0.50995 / 0.27 ( 8525) hydrogen bonds : bond 0.03585 / 2.52 ( 291) hydrogen bonds : angle 5.01819 / 3.60 ( 805) ********************** 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 54 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.186 Fit side-chains REVERT: A 173 GLU cc_start: 0.7435 (tp30) cc_final: 0.7187 (tp30) outliers start: 18 outliers final: 16 residues processed: 48 average time/residue: 0.0547 time to fit residues: 3.9337 Evaluate side-chains 51 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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 66 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 256 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 130 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 63 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.127269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.100260 restraints weight = 9712.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.103078 restraints weight = 5582.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.104734 restraints weight = 3853.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.106189 restraints weight = 3073.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.106851 restraints weight = 2596.724| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6169 Z= 0.125 Angle : 0.504 6.682 8525 Z= 0.271 Chirality : 0.041 0.144 966 Planarity : 0.003 0.040 983 Dihedral : 20.525 142.616 1116 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.47 % Allowed : 19.16 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.34), residues: 658 helix: 0.80 (0.32), residues: 272 sheet: -0.58 (0.41), residues: 168 loop : -1.08 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 95 TYR 0.008 0.001 TYR B 257 PHE 0.015 0.002 PHE A 168 TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 6169) covalent geometry : angle 0.50428 / 0.27 ( 8525) hydrogen bonds : bond 0.03542 / 2.48 ( 291) hydrogen bonds : angle 5.04325 / 3.64 ( 805) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 972.56 seconds wall clock time: 17 minutes 31.78 seconds (1051.78 seconds total)