Starting phenix.real_space_refine on Thu Jul 2 15:32:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zmi_60248/07_2026/8zmi_60248.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zmi_60248/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zmi_60248/07_2026/8zmi_60248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zmi_60248/07_2026/8zmi_60248.map" model { file = "/net/cci-nas-00/data/ceres_data/8zmi_60248/07_2026/8zmi_60248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zmi_60248/07_2026/8zmi_60248.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.04, per 1000 atoms: 0.22 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: 0.77 Conformation dependent library (CDL) restraints added in 130.9 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: 0.94 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: 1.20 Time building geometry restraints manager: 1.00 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: 13702 1.89 - 3.78: 255 3.78 - 5.68: 43 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: 1446 0.054 - 0.107: 190 0.107 - 0.161: 31 0.161 - 0.214: 8 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: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.580 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.610 ------------------------------------------------------------------------------- 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= 0.215 Angle : 0.623 9.461 14005 Z= 0.456 Chirality : 0.041 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 0.00331 / 0.22 ( 9771) covalent geometry : angle 0.62261 / 0.46 (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 : 0.166 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: 0.0754 time to fit residues: 13.9458 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 : 0.178 ------------------------------------------------------------------------------- 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 191 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.076418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.057929 restraints weight = 62449.923| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 5.49 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1485 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 : 0.578 8.317 14005 Z= 0.319 Chirality : 0.037 0.235 1678 Planarity : 0.005 0.055 1158 Dihedral : 23.481 174.600 3396 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.29 % Allowed : 9.06 % Favored : 89.64 % 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 : -0.54 (0.43), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 224 TYR 0.023 0.003 TYR A 323 PHE 0.010 0.001 PHE A 142 TRP 0.026 0.001 TRP B 102 HIS 0.005 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 9771) covalent geometry : angle 0.57826 / 0.32 (14005) hydrogen bonds : bond 0.05112 / 3.64 ( 418) hydrogen bonds : angle 4.56294 / 3.45 ( 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 : 0.170 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: 0.7287 (p90) cc_final: 0.6908 (p90) REVERT: A 77 GLN cc_start: 0.9497 (mm110) cc_final: 0.9151 (mp10) REVERT: A 110 MET cc_start: 0.9248 (tpt) cc_final: 0.8764 (tpt) REVERT: A 325 GLU cc_start: 0.9661 (pt0) cc_final: 0.9353 (pp20) REVERT: A 329 ASP cc_start: 0.9298 (m-30) cc_final: 0.9062 (m-30) REVERT: B 63 CYS cc_start: 0.9078 (m) cc_final: 0.8877 (t) REVERT: B 64 TYR cc_start: 0.8531 (t80) cc_final: 0.7950 (t80) REVERT: B 194 TYR cc_start: 0.9003 (m-80) cc_final: 0.8361 (m-80) outliers start: 8 outliers final: 4 residues processed: 97 average time/residue: 0.0633 time to fit residues: 8.9773 Evaluate side-chains 81 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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: 0.9990 chunk 67 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 81 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 36 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.077141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.058939 restraints weight = 62407.836| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 5.51 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9771 Z= 0.126 Angle : 0.529 9.956 14005 Z= 0.290 Chirality : 0.035 0.180 1678 Planarity : 0.005 0.056 1158 Dihedral : 23.491 177.283 3396 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.13 % Allowed : 12.14 % Favored : 86.73 % 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: 0.12 (0.33), residues: 694 helix: 1.05 (0.27), residues: 398 sheet: -2.59 (0.63), residues: 70 loop : -0.60 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 217 TYR 0.022 0.002 TYR B 123 PHE 0.013 0.002 PHE A 193 TRP 0.012 0.001 TRP B 102 HIS 0.008 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 9771) covalent geometry : angle 0.52910 / 0.29 (14005) hydrogen bonds : bond 0.04864 / 3.47 ( 418) hydrogen bonds : angle 4.38200 / 3.31 ( 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 87 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9492 (mm110) cc_final: 0.9171 (mp10) REVERT: A 110 MET cc_start: 0.9220 (tpt) cc_final: 0.8776 (tpt) REVERT: A 268 GLU cc_start: 0.9270 (tp30) cc_final: 0.9067 (tp30) REVERT: A 325 GLU cc_start: 0.9664 (pt0) cc_final: 0.9349 (pp20) REVERT: A 329 ASP cc_start: 0.9332 (m-30) cc_final: 0.9106 (m-30) REVERT: B 113 ASP cc_start: 0.8808 (t0) cc_final: 0.8608 (t0) REVERT: B 247 LEU cc_start: 0.9588 (mt) cc_final: 0.9194 (mp) outliers start: 7 outliers final: 5 residues processed: 86 average time/residue: 0.0672 time to fit residues: 8.6020 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 : 0.198 ------------------------------------------------------------------------------- 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 93 CYS Chi-restraints excluded: chain B residue 178 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 59 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 35 optimal weight: 0.0670 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 0.0970 chunk 38 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.077191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.058991 restraints weight = 63159.020| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 5.41 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9771 Z= 0.118 Angle : 0.521 7.911 14005 Z= 0.284 Chirality : 0.036 0.199 1678 Planarity : 0.005 0.060 1158 Dihedral : 23.449 178.676 3396 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.46 % Allowed : 13.43 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.01 (0.27), residues: 398 sheet: -2.07 (0.65), residues: 64 loop : -0.74 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 217 TYR 0.026 0.002 TYR B 123 PHE 0.012 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 0.00243 / 0.12 ( 9771) covalent geometry : angle 0.52074 / 0.28 (14005) hydrogen bonds : bond 0.04622 / 3.32 ( 418) hydrogen bonds : angle 4.28507 / 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 88 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9411 (mm110) cc_final: 0.9053 (mp10) REVERT: A 110 MET cc_start: 0.9177 (tpt) cc_final: 0.8687 (tpt) REVERT: A 325 GLU cc_start: 0.9661 (pt0) cc_final: 0.9349 (pp20) REVERT: A 329 ASP cc_start: 0.9324 (m-30) cc_final: 0.9100 (m-30) outliers start: 9 outliers final: 7 residues processed: 87 average time/residue: 0.0626 time to fit residues: 8.0518 Evaluate side-chains 76 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 93 CYS 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: 0.8980 chunk 44 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.067803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.047730 restraints weight = 53561.420| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 5.12 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9771 Z= 0.198 Angle : 0.572 8.109 14005 Z= 0.315 Chirality : 0.036 0.208 1678 Planarity : 0.005 0.060 1158 Dihedral : 23.561 178.958 3396 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.43 % Allowed : 12.46 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.07 (0.33), residues: 694 helix: 0.95 (0.27), residues: 402 sheet: -2.26 (0.65), residues: 62 loop : -0.73 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 152 TYR 0.023 0.002 TYR B 123 PHE 0.012 0.002 PHE A 35 TRP 0.012 0.002 TRP A 157 HIS 0.012 0.002 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 ( 9771) covalent geometry : angle 0.57217 / 0.32 (14005) hydrogen bonds : bond 0.05208 / 3.78 ( 418) hydrogen bonds : angle 4.37902 / 3.27 ( 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 86 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.245 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 77 GLN cc_start: 0.9512 (mm110) cc_final: 0.9169 (mp10) REVERT: A 325 GLU cc_start: 0.9663 (pt0) cc_final: 0.9370 (pp20) REVERT: A 329 ASP cc_start: 0.9261 (m-30) cc_final: 0.9057 (m-30) REVERT: B 194 TYR cc_start: 0.9047 (m-10) cc_final: 0.8277 (m-80) outliers start: 15 outliers final: 12 residues processed: 81 average time/residue: 0.0673 time to fit residues: 8.0415 Evaluate side-chains 78 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 93 CYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 254 MET 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: 1.9990 chunk 78 optimal weight: 30.0000 chunk 10 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.068187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.047932 restraints weight = 53121.667| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 5.10 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9771 Z= 0.146 Angle : 0.533 8.665 14005 Z= 0.291 Chirality : 0.036 0.180 1678 Planarity : 0.004 0.064 1158 Dihedral : 23.636 179.626 3396 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.62 % Allowed : 14.72 % Favored : 83.66 % 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: 0.11 (0.33), residues: 694 helix: 0.93 (0.27), residues: 403 sheet: -2.16 (0.67), residues: 62 loop : -0.65 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 360 TYR 0.025 0.002 TYR B 123 PHE 0.008 0.001 PHE A 359 TRP 0.008 0.001 TRP A 157 HIS 0.010 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 ( 9771) covalent geometry : angle 0.53301 / 0.29 (14005) hydrogen bonds : bond 0.04543 / 3.28 ( 418) hydrogen bonds : angle 4.29284 / 3.18 ( 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 81 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.224 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 77 GLN cc_start: 0.9499 (mm110) cc_final: 0.9141 (mp10) REVERT: A 325 GLU cc_start: 0.9664 (pt0) cc_final: 0.9367 (pp20) REVERT: A 329 ASP cc_start: 0.9260 (m-30) cc_final: 0.9052 (m-30) REVERT: B 193 PHE cc_start: 0.9226 (m-80) cc_final: 0.8856 (m-80) REVERT: B 194 TYR cc_start: 0.9072 (m-10) cc_final: 0.8235 (m-80) REVERT: B 297 TYR cc_start: 0.9065 (m-10) cc_final: 0.8479 (m-10) outliers start: 10 outliers final: 9 residues processed: 77 average time/residue: 0.0691 time to fit residues: 7.8251 Evaluate side-chains 76 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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 304 ASN Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain B residue 93 CYS 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: 0.9990 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.068864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.048635 restraints weight = 52630.668| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 5.06 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9771 Z= 0.114 Angle : 0.514 9.322 14005 Z= 0.278 Chirality : 0.035 0.211 1678 Planarity : 0.004 0.065 1158 Dihedral : 23.587 179.334 3396 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.62 % Allowed : 15.53 % 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: 0.28 (0.33), residues: 694 helix: 1.06 (0.27), residues: 403 sheet: -1.71 (0.68), residues: 64 loop : -0.69 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 224 TYR 0.023 0.002 TYR B 123 PHE 0.015 0.001 PHE B 193 TRP 0.017 0.001 TRP B 128 HIS 0.011 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 9771) covalent geometry : angle 0.51381 / 0.28 (14005) hydrogen bonds : bond 0.04362 / 3.13 ( 418) hydrogen bonds : angle 4.22888 / 3.13 ( 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 83 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.243 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 77 GLN cc_start: 0.9507 (mm110) cc_final: 0.9157 (mp10) REVERT: A 325 GLU cc_start: 0.9657 (pt0) cc_final: 0.9368 (pp20) REVERT: A 329 ASP cc_start: 0.9252 (m-30) cc_final: 0.9044 (m-30) REVERT: B 193 PHE cc_start: 0.9192 (m-80) cc_final: 0.8715 (m-80) REVERT: B 194 TYR cc_start: 0.9116 (m-10) cc_final: 0.8337 (m-80) REVERT: B 226 TYR cc_start: 0.9087 (t80) cc_final: 0.8814 (t80) REVERT: B 297 TYR cc_start: 0.9056 (m-10) cc_final: 0.8387 (m-10) outliers start: 10 outliers final: 9 residues processed: 79 average time/residue: 0.0659 time to fit residues: 7.6412 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 : 0.163 ------------------------------------------------------------------------------- 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 93 CYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 209 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: 1.9990 chunk 62 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 58 optimal weight: 0.0970 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 33 optimal weight: 3.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.069133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.048909 restraints weight = 52578.257| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 5.11 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9771 Z= 0.111 Angle : 0.518 10.437 14005 Z= 0.280 Chirality : 0.034 0.186 1678 Planarity : 0.004 0.068 1158 Dihedral : 23.539 178.958 3396 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.43 % Allowed : 15.21 % 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: 0.23 (0.33), residues: 694 helix: 1.02 (0.27), residues: 404 sheet: -2.01 (0.66), residues: 72 loop : -0.53 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 360 TYR 0.017 0.002 TYR B 64 PHE 0.013 0.001 PHE A 193 TRP 0.007 0.001 TRP B 102 HIS 0.012 0.002 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 9771) covalent geometry : angle 0.51795 / 0.28 (14005) hydrogen bonds : bond 0.04349 / 3.14 ( 418) hydrogen bonds : angle 4.18995 / 3.09 ( 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 82 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.207 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 77 GLN cc_start: 0.9503 (mm110) cc_final: 0.9162 (mp10) REVERT: A 325 GLU cc_start: 0.9647 (pt0) cc_final: 0.9372 (pp20) REVERT: B 63 CYS cc_start: 0.9383 (t) cc_final: 0.8409 (m) REVERT: B 193 PHE cc_start: 0.9222 (m-80) cc_final: 0.8604 (m-80) REVERT: B 194 TYR cc_start: 0.9122 (m-10) cc_final: 0.8296 (m-80) REVERT: B 226 TYR cc_start: 0.9007 (t80) cc_final: 0.8718 (t80) REVERT: B 297 TYR cc_start: 0.9040 (m-10) cc_final: 0.8373 (m-10) outliers start: 15 outliers final: 8 residues processed: 78 average time/residue: 0.0678 time to fit residues: 7.8396 Evaluate side-chains 73 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 93 CYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 209 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 52 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 5 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.068899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.048864 restraints weight = 51839.825| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 4.99 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9771 Z= 0.124 Angle : 0.521 10.585 14005 Z= 0.281 Chirality : 0.035 0.225 1678 Planarity : 0.004 0.069 1158 Dihedral : 23.524 178.791 3396 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % 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: 0.24 (0.33), residues: 694 helix: 1.05 (0.27), residues: 404 sheet: -1.86 (0.68), residues: 62 loop : -0.73 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.022 0.002 TYR B 64 PHE 0.013 0.001 PHE A 193 TRP 0.008 0.001 TRP A 157 HIS 0.013 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 9771) covalent geometry : angle 0.52056 / 0.28 (14005) hydrogen bonds : bond 0.04330 / 3.14 ( 418) hydrogen bonds : angle 4.22441 / 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 74 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.271 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 77 GLN cc_start: 0.9519 (mm110) cc_final: 0.9163 (mt0) REVERT: B 63 CYS cc_start: 0.9260 (t) cc_final: 0.8415 (m) REVERT: B 80 MET cc_start: 0.9378 (mmm) cc_final: 0.9173 (mmm) REVERT: B 193 PHE cc_start: 0.9261 (m-80) cc_final: 0.8675 (m-80) REVERT: B 194 TYR cc_start: 0.9135 (m-10) cc_final: 0.8331 (m-80) REVERT: B 226 TYR cc_start: 0.9007 (t80) cc_final: 0.8742 (t80) REVERT: B 254 MET cc_start: 0.6310 (OUTLIER) cc_final: 0.5667 (tpt) REVERT: B 297 TYR cc_start: 0.9036 (m-10) cc_final: 0.8408 (m-10) outliers start: 10 outliers final: 7 residues processed: 70 average time/residue: 0.0698 time to fit residues: 7.1497 Evaluate side-chains 70 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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 93 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 5 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 15 optimal weight: 0.0020 chunk 22 optimal weight: 0.0770 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 62 optimal weight: 0.0040 chunk 44 optimal weight: 4.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.069830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.049813 restraints weight = 52121.183| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 4.98 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9771 Z= 0.106 Angle : 0.533 10.931 14005 Z= 0.284 Chirality : 0.035 0.177 1678 Planarity : 0.004 0.071 1158 Dihedral : 23.487 178.369 3396 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % 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: 0.24 (0.33), residues: 694 helix: 1.09 (0.27), residues: 404 sheet: -1.99 (0.65), residues: 72 loop : -0.68 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 224 TYR 0.022 0.002 TYR B 64 PHE 0.010 0.001 PHE A 193 TRP 0.008 0.001 TRP B 102 HIS 0.012 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 ( 9771) covalent geometry : angle 0.53319 / 0.28 (14005) hydrogen bonds : bond 0.04222 / 3.04 ( 418) hydrogen bonds : angle 4.17229 / 3.07 ( 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 74 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.212 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 77 GLN cc_start: 0.9516 (mm110) cc_final: 0.9155 (mt0) REVERT: B 63 CYS cc_start: 0.9217 (t) cc_final: 0.8388 (m) REVERT: B 80 MET cc_start: 0.9408 (mmm) cc_final: 0.9176 (mmm) REVERT: B 193 PHE cc_start: 0.9263 (m-80) cc_final: 0.8659 (m-80) REVERT: B 194 TYR cc_start: 0.9144 (m-10) cc_final: 0.8544 (m-80) REVERT: B 197 MET cc_start: 0.9172 (mtm) cc_final: 0.8596 (pmm) REVERT: B 226 TYR cc_start: 0.8969 (t80) cc_final: 0.8686 (t80) REVERT: B 254 MET cc_start: 0.6013 (OUTLIER) cc_final: 0.5501 (tpt) REVERT: B 297 TYR cc_start: 0.9079 (m-10) cc_final: 0.8457 (m-10) outliers start: 9 outliers final: 7 residues processed: 71 average time/residue: 0.0736 time to fit residues: 7.4917 Evaluate side-chains 70 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 93 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 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 = 0.3818 r_free = 0.3818 target = 0.069382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.049552 restraints weight = 51410.308| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 4.95 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9771 Z= 0.115 Angle : 0.531 10.604 14005 Z= 0.286 Chirality : 0.035 0.176 1678 Planarity : 0.004 0.070 1158 Dihedral : 23.455 178.190 3396 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.62 % Allowed : 16.18 % Favored : 82.20 % 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: 1.07 (0.27), residues: 404 sheet: -2.00 (0.65), residues: 72 loop : -0.69 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 224 TYR 0.022 0.002 TYR B 64 PHE 0.011 0.001 PHE A 193 TRP 0.012 0.001 TRP B 128 HIS 0.012 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 9771) covalent geometry : angle 0.53066 / 0.29 (14005) hydrogen bonds : bond 0.04220 / 3.05 ( 418) hydrogen bonds : angle 4.14787 / 3.06 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1696.16 seconds wall clock time: 29 minutes 55.70 seconds (1795.70 seconds total)