Starting phenix.real_space_refine on Wed Aug 5 08:32:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zmi_60248/08_2026/8zmi_60248.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zmi_60248/08_2026/8zmi_60248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zmi_60248/08_2026/8zmi_60248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zmi_60248/08_2026/8zmi_60248.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zmi_60248/08_2026/8zmi_60248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zmi_60248/08_2026/8zmi_60248.map" } resolution = 3.49 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= 0.009 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: 5 Type Number sf(0) Gaussians P 171 5.49 5 S 40 5.16 5 C 5188 2.51 5 N 1598 2.21 5 O 2238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9235 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2805 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 333} Chain: "B" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2805 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 333} Chain: "C" Number of atoms: 3594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 3594 Classifications: {'RNA': 169} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 80, 'rna3p_pyr': 73} Link IDs: {'rna2p': 16, 'rna3p': 152} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.22, per 1000 atoms: 0.24 Number of scatterers: 9235 At special positions: 0 Unit cell: (89.38, 116.44, 138.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 171 15.00 O 2238 8.00 N 1598 7.00 C 5188 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: 0.96 Conformation dependent library (CDL) restraints added in 225.1 milliseconds 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1320 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 63.6% alpha, 6.4% beta 51 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 31 through 40 Processing helix chain 'A' and resid 47 through 58 Processing helix chain 'A' and resid 74 through 91 removed outlier: 3.618A pdb=" N MET A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS A 81 " --> pdb=" O GLN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 109 through 112 removed outlier: 3.714A pdb=" N GLY A 112 " --> pdb=" O LYS A 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 109 through 112' Processing helix chain 'A' and resid 113 through 132 Processing helix chain 'A' and resid 145 through 152 Processing helix chain 'A' and resid 152 through 167 Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 189 through 206 Proline residue: A 195 - end of helix removed outlier: 3.813A pdb=" N ILE A 202 " --> pdb=" O GLN A 198 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE A 203 " --> pdb=" O CYS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 230 Processing helix chain 'A' and resid 268 through 279 Processing helix chain 'A' and resid 289 through 304 removed outlier: 4.616A pdb=" N LEU A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 336 through 362 Proline residue: A 342 - end of helix Proline residue: A 354 - end of helix Processing helix chain 'A' and resid 362 through 375 Processing helix chain 'B' and resid 32 through 40 Processing helix chain 'B' and resid 47 through 58 Processing helix chain 'B' and resid 74 through 92 Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 108 through 112 removed outlier: 4.277A pdb=" N GLY B 111 " --> pdb=" O ASN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 132 Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 145 through 152 Processing helix chain 'B' and resid 156 through 167 Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 189 through 205 Proline residue: B 195 - end of helix removed outlier: 3.955A pdb=" N ILE B 202 " --> pdb=" O GLN B 198 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE B 203 " --> pdb=" O CYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 230 Processing helix chain 'B' and resid 268 through 278 Processing helix chain 'B' and resid 289 through 304 removed outlier: 4.661A pdb=" N LEU B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) Proline residue: B 301 - end of helix Processing helix chain 'B' and resid 311 through 315 removed outlier: 3.573A pdb=" N GLY B 315 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 336 through 362 Proline residue: B 342 - end of helix Proline residue: B 354 - end of helix Processing helix chain 'B' and resid 362 through 375 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 removed outlier: 3.670A pdb=" N GLU A 44 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR A 64 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN A 211 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 66 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N CYS A 63 " --> pdb=" O LYS A 96 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N TRP A 98 " --> pdb=" O CYS A 63 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP A 65 " --> pdb=" O TRP A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 306 through 308 removed outlier: 3.559A pdb=" N LYS A 318 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 44 through 46 removed outlier: 3.899A pdb=" N GLU B 44 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE B 238 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N CYS B 210 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 67 removed outlier: 6.864A pdb=" N ASP B 65 " --> pdb=" O TRP B 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 306 through 308 292 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 126 hydrogen bonds 234 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1374 1.33 - 1.45: 3328 1.45 - 1.57: 4668 1.57 - 1.69: 341 1.69 - 1.81: 60 Bond restraints: 9771 Sorted by residual: bond pdb=" N ILE B 192 " pdb=" CA ILE B 192 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.08e-02 8.57e+03 9.92e+00 bond pdb=" N ASP B 185 " pdb=" CA ASP B 185 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.27e-02 6.20e+03 9.46e+00 bond pdb=" N ILE B 178 " pdb=" CA ILE B 178 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.71e+00 bond pdb=" N CYS B 175 " pdb=" CA CYS B 175 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.35e-02 5.49e+03 7.85e+00 bond pdb=" N GLU B 186 " pdb=" CA GLU B 186 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.22e-02 6.72e+03 7.34e+00 ... (remaining 9766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 13317 1.89 - 3.78: 641 3.78 - 5.68: 42 5.68 - 7.57: 1 7.57 - 9.46: 4 Bond angle restraints: 14005 Sorted by residual: angle pdb=" N ILE B 192 " pdb=" CA ILE B 192 " pdb=" C ILE B 192 " ideal model delta sigma weight residual 113.42 104.22 9.20 1.17e+00 7.31e-01 6.18e+01 angle pdb=" O2 C C 112 " pdb=" C2 C C 112 " pdb=" N3 C C 112 " ideal model delta sigma weight residual 121.90 116.70 5.20 7.00e-01 2.04e+00 5.52e+01 angle pdb=" N ASP A 229 " pdb=" CA ASP A 229 " pdb=" C ASP A 229 " ideal model delta sigma weight residual 113.50 105.33 8.17 1.23e+00 6.61e-01 4.41e+01 angle pdb=" N1 C C 112 " pdb=" C2 C C 112 " pdb=" O2 C C 112 " ideal model delta sigma weight residual 118.90 122.56 -3.66 6.00e-01 2.78e+00 3.72e+01 angle pdb=" N1 C C 98 " pdb=" C2 C C 98 " pdb=" O2 C C 98 " ideal model delta sigma weight residual 118.90 121.95 -3.05 6.00e-01 2.78e+00 2.58e+01 ... (remaining 14000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.03: 5597 35.03 - 70.06: 515 70.06 - 105.09: 70 105.09 - 140.13: 1 140.13 - 175.16: 5 Dihedral angle restraints: 6188 sinusoidal: 4150 harmonic: 2038 Sorted by residual: dihedral pdb=" O4' U C 67 " pdb=" C1' U C 67 " pdb=" N1 U C 67 " pdb=" C2 U C 67 " ideal model delta sinusoidal sigma weight residual 200.00 41.69 158.31 1 1.50e+01 4.44e-03 8.23e+01 dihedral pdb=" O4' U C 45 " pdb=" C1' U C 45 " pdb=" N1 U C 45 " pdb=" C2 U C 45 " ideal model delta sinusoidal sigma weight residual 200.00 42.20 157.80 1 1.50e+01 4.44e-03 8.22e+01 dihedral pdb=" O4' C C 68 " pdb=" C1' C C 68 " pdb=" N1 C C 68 " pdb=" C2 C C 68 " ideal model delta sinusoidal sigma weight residual 200.00 51.51 148.49 1 1.50e+01 4.44e-03 7.90e+01 ... (remaining 6185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1293 0.054 - 0.107: 206 0.107 - 0.161: 169 0.161 - 0.214: 7 0.214 - 0.268: 3 Chirality restraints: 1678 Sorted by residual: chirality pdb=" P G C 46 " pdb=" OP1 G C 46 " pdb=" OP2 G C 46 " pdb=" O5' G C 46 " both_signs ideal model delta sigma weight residual True 2.41 -2.68 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA THR B 188 " pdb=" N THR B 188 " pdb=" C THR B 188 " pdb=" CB THR B 188 " both_signs ideal model delta sigma weight residual False 2.53 2.79 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA GLU B 183 " pdb=" N GLU B 183 " pdb=" C GLU B 183 " pdb=" CB GLU B 183 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1675 not shown) Planarity restraints: 1158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 174 " -0.017 2.00e-02 2.50e+03 3.38e-02 1.15e+01 pdb=" C ARG B 174 " 0.059 2.00e-02 2.50e+03 pdb=" O ARG B 174 " -0.022 2.00e-02 2.50e+03 pdb=" N CYS B 175 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 102 " -0.027 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" CG TRP B 102 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP B 102 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 102 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 102 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 102 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 102 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 102 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 102 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 102 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 226 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C TYR A 226 " 0.055 2.00e-02 2.50e+03 pdb=" O TYR A 226 " -0.021 2.00e-02 2.50e+03 pdb=" N CYS A 227 " -0.018 2.00e-02 2.50e+03 ... (remaining 1155 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 419 2.70 - 3.25: 8866 3.25 - 3.80: 16921 3.80 - 4.35: 21009 4.35 - 4.90: 31102 Nonbonded interactions: 78317 Sorted by model distance: nonbonded pdb=" O LYS B 277 " pdb=" O2' U C 23 " model vdw 2.146 3.040 nonbonded pdb=" OD1 ASP B 101 " pdb=" OG SER B 145 " model vdw 2.178 3.040 nonbonded pdb=" O PRO B 282 " pdb=" OH TYR B 330 " model vdw 2.198 3.040 nonbonded pdb=" O GLY B 66 " pdb=" O3' ATP B 401 " model vdw 2.214 3.040 nonbonded pdb=" OG SER A 332 " pdb=" OE1 GLU A 334 " model vdw 2.223 3.040 ... (remaining 78312 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' selection = (chain 'B' and resid 31 through 379) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.080 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6174 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 : 0.003 0.039 9771 Z= 0.230 Angle : 0.746 9.461 14005 Z= 0.557 Chirality : 0.056 0.268 1678 Planarity : 0.005 0.070 1158 Dihedral : 22.149 175.157 4868 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.59 % Favored : 97.12 % Rotamer: Outliers : 0.16 % Allowed : 0.32 % Favored : 99.51 % 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: 694 helix: 1.16 (0.27), residues: 405 sheet: -1.70 (0.66), residues: 71 loop : -0.69 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 224 TYR 0.012 0.002 TYR B 123 PHE 0.015 0.002 PHE B 193 TRP 0.057 0.002 TRP B 102 HIS 0.004 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.23 ( 9771) covalent geometry : angle 0.74605 / 0.56 (14005) hydrogen bonds : bond 0.10096 / 6.90 ( 418) hydrogen bonds : angle 4.86581 / 3.65 ( 1086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.5520 (p90) cc_final: 0.5229 (p90) outliers start: 1 outliers final: 1 residues processed: 132 average time/residue: 0.0994 time to fit residues: 18.4447 Evaluate side-chains 85 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.076453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.057948 restraints weight = 62477.255| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 5.47 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9771 Z= 0.141 Angle : 0.593 8.525 14005 Z= 0.322 Chirality : 0.038 0.282 1678 Planarity : 0.005 0.054 1158 Dihedral : 23.357 174.591 3396 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.29 % Allowed : 9.22 % Favored : 89.48 % 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: 0.19 (0.33), residues: 694 helix: 1.13 (0.27), residues: 396 sheet: -2.41 (0.60), residues: 81 loop : -0.55 (0.43), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 224 TYR 0.023 0.003 TYR B 323 PHE 0.012 0.001 PHE A 142 TRP 0.026 0.001 TRP B 102 HIS 0.006 0.002 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 9771) covalent geometry : angle 0.59337 / 0.32 (14005) hydrogen bonds : bond 0.05237 / 3.73 ( 418) hydrogen bonds : angle 4.56947 / 3.46 ( 1086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.7294 (p90) cc_final: 0.6871 (p90) REVERT: A 110 MET cc_start: 0.9250 (tpt) cc_final: 0.8773 (tpt) REVERT: A 325 GLU cc_start: 0.9661 (pt0) cc_final: 0.9356 (pp20) REVERT: A 329 ASP cc_start: 0.9298 (m-30) cc_final: 0.9056 (m-30) REVERT: B 64 TYR cc_start: 0.8531 (t80) cc_final: 0.7918 (t80) REVERT: B 194 TYR cc_start: 0.8997 (m-80) cc_final: 0.8353 (m-80) REVERT: B 222 LEU cc_start: 0.9842 (tp) cc_final: 0.9642 (mp) outliers start: 8 outliers final: 4 residues processed: 97 average time/residue: 0.0904 time to fit residues: 12.8409 Evaluate side-chains 80 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 209 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 60 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 36 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 GLN A 358 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.077375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.059178 restraints weight = 62406.045| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 5.38 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9771 Z= 0.120 Angle : 0.542 11.552 14005 Z= 0.293 Chirality : 0.036 0.279 1678 Planarity : 0.005 0.055 1158 Dihedral : 23.348 177.086 3396 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.13 % Allowed : 11.33 % Favored : 87.54 % 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: 0.14 (0.33), residues: 694 helix: 1.04 (0.27), residues: 398 sheet: -2.29 (0.67), residues: 61 loop : -0.73 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 217 TYR 0.022 0.003 TYR B 123 PHE 0.014 0.002 PHE A 193 TRP 0.013 0.001 TRP B 102 HIS 0.009 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 9771) covalent geometry : angle 0.54164 / 0.29 (14005) hydrogen bonds : bond 0.04984 / 3.56 ( 418) hydrogen bonds : angle 4.37004 / 3.29 ( 1086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9486 (mm110) cc_final: 0.9168 (mp10) REVERT: A 110 MET cc_start: 0.9202 (tpt) cc_final: 0.8774 (tpt) REVERT: A 268 GLU cc_start: 0.9303 (tp30) cc_final: 0.9084 (tp30) REVERT: A 325 GLU cc_start: 0.9656 (pt0) cc_final: 0.9344 (pp20) REVERT: A 329 ASP cc_start: 0.9255 (m-30) cc_final: 0.9041 (m-30) REVERT: B 63 CYS cc_start: 0.8890 (t) cc_final: 0.8423 (t) REVERT: B 113 ASP cc_start: 0.8725 (t0) cc_final: 0.8520 (t0) REVERT: B 214 MET cc_start: 0.8389 (mmm) cc_final: 0.8110 (mmm) REVERT: B 247 LEU cc_start: 0.9582 (mt) cc_final: 0.9190 (mp) outliers start: 7 outliers final: 5 residues processed: 85 average time/residue: 0.0850 time to fit residues: 10.7040 Evaluate side-chains 79 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 209 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 35 optimal weight: 0.0980 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 chunk 38 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.0060 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 ASN ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.071634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.051277 restraints weight = 51886.671| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 5.08 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9771 Z= 0.114 Angle : 0.540 9.034 14005 Z= 0.290 Chirality : 0.036 0.283 1678 Planarity : 0.005 0.059 1158 Dihedral : 23.297 178.184 3396 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.46 % Allowed : 13.27 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.04 (0.33), residues: 694 helix: 0.95 (0.27), residues: 398 sheet: -2.53 (0.58), residues: 82 loop : -0.45 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 217 TYR 0.025 0.002 TYR B 123 PHE 0.018 0.001 PHE A 359 TRP 0.009 0.001 TRP B 102 HIS 0.010 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 9771) covalent geometry : angle 0.53999 / 0.29 (14005) hydrogen bonds : bond 0.04743 / 3.40 ( 418) hydrogen bonds : angle 4.28222 / 3.20 ( 1086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9458 (mm110) cc_final: 0.9111 (mp10) REVERT: A 110 MET cc_start: 0.9185 (tpt) cc_final: 0.8752 (tpt) REVERT: A 133 MET cc_start: 0.7005 (mmm) cc_final: 0.6155 (mmm) REVERT: A 268 GLU cc_start: 0.9277 (tp30) cc_final: 0.9072 (tp30) REVERT: A 325 GLU cc_start: 0.9642 (pt0) cc_final: 0.9343 (pp20) REVERT: A 329 ASP cc_start: 0.9184 (m-30) cc_final: 0.8976 (m-30) outliers start: 9 outliers final: 6 residues processed: 90 average time/residue: 0.0842 time to fit residues: 11.3299 Evaluate side-chains 77 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 209 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 83 optimal weight: 30.0000 chunk 32 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.067111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.046880 restraints weight = 54051.290| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 5.13 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9771 Z= 0.220 Angle : 0.604 7.770 14005 Z= 0.326 Chirality : 0.038 0.256 1678 Planarity : 0.005 0.061 1158 Dihedral : 23.431 178.256 3396 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.10 % Allowed : 14.56 % Favored : 83.33 % 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: -0.01 (0.33), residues: 694 helix: 0.87 (0.27), residues: 402 sheet: -2.20 (0.66), residues: 62 loop : -0.78 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 152 TYR 0.024 0.003 TYR B 123 PHE 0.014 0.002 PHE A 35 TRP 0.012 0.002 TRP A 302 HIS 0.012 0.003 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.22 ( 9771) covalent geometry : angle 0.60412 / 0.33 (14005) hydrogen bonds : bond 0.05544 / 4.02 ( 418) hydrogen bonds : angle 4.43147 / 3.29 ( 1086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9518 (mm110) cc_final: 0.9167 (mp10) REVERT: A 133 MET cc_start: 0.7724 (mmm) cc_final: 0.7421 (mmm) REVERT: A 325 GLU cc_start: 0.9661 (pt0) cc_final: 0.9371 (pp20) REVERT: A 329 ASP cc_start: 0.9254 (m-30) cc_final: 0.9045 (m-30) REVERT: B 194 TYR cc_start: 0.9067 (m-10) cc_final: 0.8248 (m-80) outliers start: 13 outliers final: 10 residues processed: 77 average time/residue: 0.0823 time to fit residues: 9.5405 Evaluate side-chains 74 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 355 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 39 optimal weight: 0.7980 chunk 78 optimal weight: 40.0000 chunk 10 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 358 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 = 0.3795 r_free = 0.3795 target = 0.068830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.048505 restraints weight = 52455.769| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 5.04 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9771 Z= 0.123 Angle : 0.533 8.864 14005 Z= 0.287 Chirality : 0.036 0.270 1678 Planarity : 0.004 0.064 1158 Dihedral : 23.498 179.296 3396 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.29 % Allowed : 15.53 % Favored : 83.17 % 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: 0.15 (0.33), residues: 694 helix: 0.98 (0.27), residues: 402 sheet: -1.85 (0.67), residues: 64 loop : -0.74 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 360 TYR 0.024 0.002 TYR B 123 PHE 0.019 0.001 PHE B 193 TRP 0.006 0.001 TRP A 102 HIS 0.011 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 9771) covalent geometry : angle 0.53341 / 0.29 (14005) hydrogen bonds : bond 0.04550 / 3.26 ( 418) hydrogen bonds : angle 4.24210 / 3.12 ( 1086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9501 (mm110) cc_final: 0.9152 (mp10) REVERT: A 133 MET cc_start: 0.7686 (mmm) cc_final: 0.7440 (mmm) REVERT: A 325 GLU cc_start: 0.9660 (pt0) cc_final: 0.9355 (pp20) REVERT: A 329 ASP cc_start: 0.9249 (m-30) cc_final: 0.9032 (m-30) REVERT: B 193 PHE cc_start: 0.9162 (m-80) cc_final: 0.8772 (m-80) REVERT: B 297 TYR cc_start: 0.9050 (m-10) cc_final: 0.8466 (m-10) outliers start: 8 outliers final: 7 residues processed: 76 average time/residue: 0.0894 time to fit residues: 10.1464 Evaluate side-chains 75 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 254 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 74 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.069203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.048969 restraints weight = 52697.075| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 5.12 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9771 Z= 0.112 Angle : 0.527 9.953 14005 Z= 0.281 Chirality : 0.035 0.270 1678 Planarity : 0.004 0.066 1158 Dihedral : 23.451 179.831 3396 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.29 % Allowed : 15.86 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.26 (0.33), residues: 694 helix: 1.04 (0.27), residues: 403 sheet: -1.75 (0.68), residues: 64 loop : -0.69 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 224 TYR 0.030 0.002 TYR B 123 PHE 0.011 0.001 PHE B 193 TRP 0.012 0.001 TRP B 128 HIS 0.011 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 9771) covalent geometry : angle 0.52716 / 0.28 (14005) hydrogen bonds : bond 0.04490 / 3.24 ( 418) hydrogen bonds : angle 4.19971 / 3.09 ( 1086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9508 (mm110) cc_final: 0.9165 (mp10) REVERT: A 133 MET cc_start: 0.7752 (mmm) cc_final: 0.7534 (mmm) REVERT: A 325 GLU cc_start: 0.9660 (pt0) cc_final: 0.9373 (pp20) REVERT: B 193 PHE cc_start: 0.9126 (m-80) cc_final: 0.8491 (m-80) REVERT: B 194 TYR cc_start: 0.9139 (m-80) cc_final: 0.8368 (m-80) REVERT: B 226 TYR cc_start: 0.9049 (t80) cc_final: 0.8839 (t80) REVERT: B 297 TYR cc_start: 0.9042 (m-10) cc_final: 0.8440 (m-10) outliers start: 8 outliers final: 6 residues processed: 76 average time/residue: 0.0834 time to fit residues: 9.4695 Evaluate side-chains 73 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 254 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 ASN ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.069055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.048929 restraints weight = 51970.373| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 5.05 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9771 Z= 0.122 Angle : 0.529 10.071 14005 Z= 0.284 Chirality : 0.035 0.272 1678 Planarity : 0.004 0.068 1158 Dihedral : 23.434 179.421 3396 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.13 % Allowed : 16.83 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.25 (0.33), residues: 694 helix: 1.03 (0.27), residues: 404 sheet: -1.63 (0.68), residues: 64 loop : -0.71 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 360 TYR 0.026 0.002 TYR B 123 PHE 0.009 0.001 PHE B 193 TRP 0.010 0.001 TRP B 128 HIS 0.012 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 9771) covalent geometry : angle 0.52886 / 0.28 (14005) hydrogen bonds : bond 0.04463 / 3.23 ( 418) hydrogen bonds : angle 4.21646 / 3.10 ( 1086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9522 (mm110) cc_final: 0.9172 (mt0) REVERT: A 133 MET cc_start: 0.7680 (mmm) cc_final: 0.7458 (mmm) REVERT: B 193 PHE cc_start: 0.9220 (m-80) cc_final: 0.8583 (m-80) REVERT: B 194 TYR cc_start: 0.9161 (m-80) cc_final: 0.8389 (m-80) REVERT: B 214 MET cc_start: 0.8366 (mmm) cc_final: 0.8132 (mmp) REVERT: B 226 TYR cc_start: 0.9004 (t80) cc_final: 0.8739 (t80) REVERT: B 297 TYR cc_start: 0.9056 (m-10) cc_final: 0.8405 (m-10) outliers start: 7 outliers final: 7 residues processed: 71 average time/residue: 0.0846 time to fit residues: 8.8999 Evaluate side-chains 72 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 254 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 358 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 = 0.3774 r_free = 0.3774 target = 0.067909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.047713 restraints weight = 52446.031| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 5.01 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9771 Z= 0.145 Angle : 0.547 10.586 14005 Z= 0.291 Chirality : 0.035 0.268 1678 Planarity : 0.004 0.068 1158 Dihedral : 23.462 179.221 3396 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.46 % Allowed : 16.18 % Favored : 82.36 % 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: 0.22 (0.33), residues: 694 helix: 1.03 (0.27), residues: 404 sheet: -1.92 (0.68), residues: 62 loop : -0.70 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.026 0.002 TYR B 123 PHE 0.017 0.001 PHE A 320 TRP 0.009 0.001 TRP B 128 HIS 0.012 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 9771) covalent geometry : angle 0.54721 / 0.29 (14005) hydrogen bonds : bond 0.04552 / 3.31 ( 418) hydrogen bonds : angle 4.24817 / 3.12 ( 1086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9529 (mm110) cc_final: 0.9180 (mt0) REVERT: A 133 MET cc_start: 0.7870 (mmm) cc_final: 0.7648 (mmm) REVERT: B 63 CYS cc_start: 0.9094 (t) cc_final: 0.8814 (m) REVERT: B 193 PHE cc_start: 0.9234 (m-80) cc_final: 0.8626 (m-80) REVERT: B 194 TYR cc_start: 0.9158 (m-80) cc_final: 0.8559 (m-80) REVERT: B 197 MET cc_start: 0.9212 (mtm) cc_final: 0.8630 (pmm) REVERT: B 226 TYR cc_start: 0.9035 (t80) cc_final: 0.8754 (t80) REVERT: B 297 TYR cc_start: 0.9055 (m-10) cc_final: 0.8398 (m-80) outliers start: 9 outliers final: 6 residues processed: 72 average time/residue: 0.0912 time to fit residues: 9.6341 Evaluate side-chains 70 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 254 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 5 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 ASN A 358 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.066204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.046024 restraints weight = 53993.860| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 5.01 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9771 Z= 0.172 Angle : 0.577 11.027 14005 Z= 0.311 Chirality : 0.036 0.262 1678 Planarity : 0.005 0.071 1158 Dihedral : 23.622 178.757 3396 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.62 % Allowed : 15.86 % Favored : 82.52 % 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: 0.17 (0.32), residues: 694 helix: 1.02 (0.27), residues: 404 sheet: -1.84 (0.67), residues: 60 loop : -0.82 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 152 TYR 0.027 0.002 TYR B 64 PHE 0.011 0.002 PHE A 35 TRP 0.012 0.002 TRP A 157 HIS 0.010 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 ( 9771) covalent geometry : angle 0.57652 / 0.31 (14005) hydrogen bonds : bond 0.05010 / 3.66 ( 418) hydrogen bonds : angle 4.32171 / 3.16 ( 1086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9547 (mm110) cc_final: 0.9203 (mp10) REVERT: A 110 MET cc_start: 0.9405 (tpt) cc_final: 0.9114 (tpt) REVERT: A 133 MET cc_start: 0.8021 (mmm) cc_final: 0.7731 (mmm) REVERT: B 193 PHE cc_start: 0.9265 (m-80) cc_final: 0.8735 (m-80) REVERT: B 194 TYR cc_start: 0.9161 (m-80) cc_final: 0.8414 (m-80) REVERT: B 226 TYR cc_start: 0.9094 (t80) cc_final: 0.8832 (t80) REVERT: B 297 TYR cc_start: 0.9105 (m-10) cc_final: 0.8481 (m-80) outliers start: 10 outliers final: 7 residues processed: 71 average time/residue: 0.0788 time to fit residues: 8.3643 Evaluate side-chains 67 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 68 optimal weight: 30.0000 chunk 46 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.067648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.047443 restraints weight = 52303.613| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 5.06 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9771 Z= 0.117 Angle : 0.545 10.697 14005 Z= 0.292 Chirality : 0.035 0.275 1678 Planarity : 0.004 0.070 1158 Dihedral : 23.610 177.937 3396 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.97 % Allowed : 17.48 % Favored : 81.55 % 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: 0.29 (0.32), residues: 694 helix: 1.08 (0.27), residues: 404 sheet: -1.52 (0.67), residues: 62 loop : -0.79 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 371 TYR 0.024 0.002 TYR B 123 PHE 0.008 0.001 PHE B 142 TRP 0.010 0.001 TRP B 102 HIS 0.013 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 9771) covalent geometry : angle 0.54473 / 0.29 (14005) hydrogen bonds : bond 0.04501 / 3.25 ( 418) hydrogen bonds : angle 4.23174 / 3.10 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2181.68 seconds wall clock time: 38 minutes 21.20 seconds (2301.20 seconds total)