Starting phenix.real_space_refine on Tue Mar 11 14:30:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p8v_13255/03_2025/7p8v_13255.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p8v_13255/03_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_13255/03_2025/7p8v_13255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p8v_13255/03_2025/7p8v_13255.map" model { file = "/net/cci-nas-00/data/ceres_data/7p8v_13255/03_2025/7p8v_13255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p8v_13255/03_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-5624/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: 4.43, per 1000 atoms: 0.74 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: 1.55 Conformation dependent library (CDL) restraints added in 770.9 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: 2.15 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: 1.81 Time building geometry restraints manager: 1.81 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.290 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.160 ------------------------------------------------------------------------------- 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 : 0.667 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: 0.2198 time to fit residues: 22.3964 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 : 0.636 ------------------------------------------------------------------------------- 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 = 3921.505| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- 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 : 0.620 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.1532 time to fit residues: 14.6085 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 : 0.577 ------------------------------------------------------------------------------- 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: 0.3980 chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.127971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.101299 restraints weight = 9678.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.102651 restraints weight = 6130.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.104895 restraints weight = 4373.777| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2330 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= 0.211 Angle : 0.538 6.348 8525 Z= 0.295 Chirality : 0.042 0.147 966 Planarity : 0.004 0.039 983 Dihedral : 20.744 136.682 1172 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.19 % Allowed : 15.69 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.33), residues: 658 helix: 0.86 (0.32), residues: 272 sheet: -0.38 (0.40), residues: 158 loop : -1.16 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.004 0.001 HIS B 308 PHE 0.017 0.002 PHE A 168 TYR 0.009 0.001 TYR B 323 ARG 0.004 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 65 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7681 (tp30) cc_final: 0.7393 (tp30) outliers start: 12 outliers final: 8 residues processed: 59 average time/residue: 0.1673 time to fit residues: 13.6688 Evaluate side-chains 50 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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: 4.9990 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 0.0670 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 8 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.0722 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.126996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.099780 restraints weight = 9768.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.102581 restraints weight = 5578.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.104382 restraints weight = 3847.652| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2623 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= 0.226 Angle : 0.528 6.387 8525 Z= 0.286 Chirality : 0.041 0.149 966 Planarity : 0.004 0.040 983 Dihedral : 20.621 140.473 1172 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.10 % Allowed : 16.79 % 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: -0.30 (0.34), residues: 658 helix: 0.89 (0.33), residues: 272 sheet: -0.72 (0.40), residues: 168 loop : -0.99 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.004 0.001 HIS B 308 PHE 0.018 0.002 PHE A 168 TYR 0.010 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 63 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7693 (tp30) cc_final: 0.7380 (tp30) outliers start: 17 outliers final: 13 residues processed: 58 average time/residue: 0.1606 time to fit residues: 12.9105 Evaluate side-chains 55 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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: 0.9980 chunk 35 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.128640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.102406 restraints weight = 9594.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104629 restraints weight = 6138.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.105315 restraints weight = 3979.140| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6169 Z= 0.174 Angle : 0.501 6.491 8525 Z= 0.270 Chirality : 0.040 0.142 966 Planarity : 0.004 0.040 983 Dihedral : 20.459 141.076 1172 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.01 % Allowed : 16.42 % 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: -0.19 (0.34), residues: 658 helix: 0.89 (0.33), residues: 272 sheet: -0.52 (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 0.011 0.001 PHE A 168 TYR 0.008 0.001 TYR B 257 ARG 0.003 0.000 ARG B 128 *********************** 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 67 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 0.650 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 61 average time/residue: 0.1966 time to fit residues: 15.7963 Evaluate side-chains 48 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.125888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.098385 restraints weight = 9567.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.101431 restraints weight = 5208.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.103467 restraints weight = 3483.994| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 6169 Z= 0.285 Angle : 0.544 6.255 8525 Z= 0.294 Chirality : 0.041 0.152 966 Planarity : 0.004 0.040 983 Dihedral : 20.481 144.169 1172 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.47 % Allowed : 18.07 % Favored : 78.47 % 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: -0.32 (0.34), residues: 658 helix: 0.81 (0.33), residues: 272 sheet: -0.64 (0.40), residues: 168 loop : -1.00 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 229 HIS 0.004 0.001 HIS B 304 PHE 0.022 0.002 PHE A 168 TYR 0.010 0.001 TYR B 257 ARG 0.006 0.000 ARG A 162 *********************** 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 58 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 0.635 Fit side-chains outliers start: 19 outliers final: 15 residues processed: 52 average time/residue: 0.1487 time to fit residues: 11.2424 Evaluate side-chains 51 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 60 optimal weight: 0.0020 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.121827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.092348 restraints weight = 9915.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.095587 restraints weight = 5187.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.097767 restraints weight = 3397.951| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6169 Z= 0.167 Angle : 0.487 6.130 8525 Z= 0.263 Chirality : 0.040 0.142 966 Planarity : 0.003 0.043 983 Dihedral : 20.267 144.759 1172 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.65 % Allowed : 18.07 % 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: -0.12 (0.34), residues: 658 helix: 0.92 (0.33), residues: 272 sheet: -0.45 (0.41), residues: 164 loop : -0.90 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 229 HIS 0.003 0.001 HIS A 308 PHE 0.009 0.001 PHE B 168 TYR 0.008 0.001 TYR B 257 ARG 0.003 0.000 ARG A 162 *********************** 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 59 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 39 time to evaluate : 0.632 Fit side-chains outliers start: 20 outliers final: 14 residues processed: 53 average time/residue: 0.1744 time to fit residues: 12.7802 Evaluate side-chains 48 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 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 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 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: 0.9980 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 = 0.3635 r_free = 0.3635 target = 0.120937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.091743 restraints weight = 9896.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.094909 restraints weight = 5146.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.097065 restraints weight = 3382.389| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3270 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= 0.191 Angle : 0.507 8.407 8525 Z= 0.271 Chirality : 0.040 0.147 966 Planarity : 0.004 0.043 983 Dihedral : 20.216 146.333 1172 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.92 % Allowed : 19.16 % 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: -0.16 (0.34), residues: 658 helix: 0.89 (0.33), residues: 272 sheet: -0.55 (0.41), residues: 168 loop : -0.85 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.004 0.001 HIS B 308 PHE 0.016 0.002 PHE A 168 TYR 0.008 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 55 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.637 Fit side-chains REVERT: B 308 HIS cc_start: 0.7777 (m-70) cc_final: 0.7479 (m90) outliers start: 16 outliers final: 14 residues processed: 49 average time/residue: 0.1776 time to fit residues: 12.0842 Evaluate side-chains 49 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 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 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 262 MET 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: 0.6980 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.117369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.088383 restraints weight = 10118.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.091509 restraints weight = 5298.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.093644 restraints weight = 3491.623| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 6169 Z= 0.358 Angle : 0.595 6.478 8525 Z= 0.318 Chirality : 0.043 0.157 966 Planarity : 0.004 0.043 983 Dihedral : 20.360 151.160 1172 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.92 % Allowed : 19.16 % 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: -0.33 (0.34), residues: 658 helix: 0.76 (0.33), residues: 270 sheet: -0.62 (0.40), residues: 168 loop : -0.95 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 229 HIS 0.005 0.001 HIS B 75 PHE 0.027 0.003 PHE A 168 TYR 0.015 0.002 TYR B 291 ARG 0.005 0.001 ARG A 162 *********************** 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 58 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.576 Fit side-chains outliers start: 16 outliers final: 15 residues processed: 51 average time/residue: 0.1792 time to fit residues: 12.4910 Evaluate side-chains 51 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 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 262 MET 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: 0.6980 chunk 29 optimal weight: 0.4980 chunk 53 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN B 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.121891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.091816 restraints weight = 10019.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.094905 restraints weight = 5408.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.096999 restraints weight = 3641.225| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3364 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= 0.175 Angle : 0.508 6.602 8525 Z= 0.273 Chirality : 0.040 0.144 966 Planarity : 0.004 0.043 983 Dihedral : 20.156 146.703 1172 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.92 % Allowed : 18.98 % 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: -0.26 (0.34), residues: 658 helix: 0.83 (0.33), residues: 272 sheet: -0.58 (0.41), residues: 168 loop : -0.95 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS A 308 PHE 0.011 0.001 PHE B 168 TYR 0.009 0.001 TYR B 257 ARG 0.003 0.000 ARG B 273 ********************** 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: 16 poor density : 38 time to evaluate : 0.642 Fit side-chains REVERT: A 173 GLU cc_start: 0.7846 (tp30) cc_final: 0.7530 (tp30) outliers start: 16 outliers final: 14 residues processed: 48 average time/residue: 0.1852 time to fit residues: 12.1726 Evaluate side-chains 49 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 94 PHE 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 122 GLN Chi-restraints excluded: chain B residue 143 THR 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: 0.5980 chunk 37 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.122090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.091921 restraints weight = 10226.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.095036 restraints weight = 5488.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.097164 restraints weight = 3670.846| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3397 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= 0.179 Angle : 0.509 6.229 8525 Z= 0.272 Chirality : 0.040 0.144 966 Planarity : 0.004 0.044 983 Dihedral : 20.115 147.364 1172 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.55 % Allowed : 18.98 % Favored : 78.47 % 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: -0.57 (0.41), residues: 168 loop : -0.94 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS A 308 PHE 0.012 0.001 PHE A 168 TYR 0.010 0.001 TYR B 124 ARG 0.002 0.000 ARG B 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1858.06 seconds wall clock time: 32 minutes 53.57 seconds (1973.57 seconds total)