Starting phenix.real_space_refine on Thu Sep 10 21:41:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6lz0_30020/09_2026/6lz0_30020.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lz0_30020/09_2026/6lz0_30020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lz0_30020/09_2026/6lz0_30020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lz0_30020/09_2026/6lz0_30020.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lz0_30020/09_2026/6lz0_30020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lz0_30020/09_2026/6lz0_30020.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6lz0_30020/09_2026/6lz0_30020.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6lz0_30020/09_2026/6lz0_30020.cif" } resolution = 3.3 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= 0.007 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: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 2604 2.51 5 N 679 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4006 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2846 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 17, 'TRANS': 357} Chain breaks: 1 Chain: "B" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1154 Classifications: {'peptide': 216} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 161} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 205} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 550 Unresolved non-hydrogen angles: 705 Unresolved non-hydrogen dihedrals: 460 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'PHE:plan': 5, 'GLU:plan': 16, 'ASP:plan': 12, 'ASN:plan1': 7, 'HIS:plan': 3, 'ARG:plan': 7, 'TRP:plan': 4, 'GLN:plan1': 6, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 289 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'2OP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.33, per 1000 atoms: 0.33 Number of scatterers: 4006 At special positions: 0 Unit cell: (106.526, 58.698, 118.483, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 698 8.00 N 679 7.00 C 2604 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: 0.42 Conformation dependent library (CDL) restraints added in 186.1 milliseconds 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1054 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 4 sheets defined 63.3% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 18 through 35 removed outlier: 4.194A pdb=" N VAL A 22 " --> pdb=" O TRP A 18 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL A 23 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 24 " --> pdb=" O TRP A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 41 removed outlier: 3.680A pdb=" N THR A 41 " --> pdb=" O PRO A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 54 through 84 removed outlier: 5.185A pdb=" N ILE A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 85 through 104 Processing helix chain 'A' and resid 109 through 139 removed outlier: 3.895A pdb=" N VAL A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ILE A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) Proline residue: A 130 - end of helix removed outlier: 3.780A pdb=" N THR A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.629A pdb=" N ALA A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Proline residue: A 155 - end of helix removed outlier: 4.510A pdb=" N ALA A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 173 through 193 removed outlier: 4.364A pdb=" N GLY A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 274 removed outlier: 3.884A pdb=" N ILE A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 291 removed outlier: 5.655A pdb=" N SER A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN A 291 " --> pdb=" O TYR A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 320 removed outlier: 3.937A pdb=" N VAL A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Proline residue: A 314 - end of helix Processing helix chain 'A' and resid 321 through 326 Proline residue: A 324 - end of helix No H-bonds generated for 'chain 'A' and resid 321 through 326' Processing helix chain 'A' and resid 330 through 345 removed outlier: 3.635A pdb=" N ALA A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N SER A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 337 " --> pdb=" O PHE A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 383 removed outlier: 3.569A pdb=" N VAL A 358 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N PHE A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET A 379 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.738A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 405 removed outlier: 3.731A pdb=" N VAL A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 416 removed outlier: 4.457A pdb=" N ARG A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 448 removed outlier: 4.257A pdb=" N TRP A 424 " --> pdb=" O LYS A 420 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A 428 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N MET A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 153 through 156 Processing helix chain 'B' and resid 205 through 238 Proline residue: B 211 - end of helix Proline residue: B 235 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 33 Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 removed outlier: 4.067A pdb=" N GLY B 95 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.501A pdb=" N ARG B 166 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 113 through 117 removed outlier: 6.316A pdb=" N GLU B 114 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ARG B 203 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE B 116 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 192 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TRP B 139 " --> pdb=" O LEU B 150 " (cutoff:3.500A) 281 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.52 Time building geometry restraints manager: 0.55 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: 794 1.33 - 1.45: 986 1.45 - 1.57: 2273 1.57 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 4091 Sorted by residual: bond pdb=" CA VAL B 131 " pdb=" C VAL B 131 " ideal model delta sigma weight residual 1.524 1.557 -0.033 8.30e-03 1.45e+04 1.63e+01 bond pdb=" N ARG A 326 " pdb=" CA ARG A 326 " ideal model delta sigma weight residual 1.462 1.489 -0.027 8.50e-03 1.38e+04 1.03e+01 bond pdb=" C ASP B 179 " pdb=" N PRO B 180 " ideal model delta sigma weight residual 1.332 1.366 -0.034 1.12e-02 7.97e+03 9.43e+00 bond pdb=" N GLU B 120 " pdb=" CA GLU B 120 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.31e-02 5.83e+03 8.95e+00 bond pdb=" N GLY B 103 " pdb=" CA GLY B 103 " ideal model delta sigma weight residual 1.443 1.483 -0.041 1.37e-02 5.33e+03 8.87e+00 ... (remaining 4086 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 4992 1.77 - 3.54: 471 3.54 - 5.30: 97 5.30 - 7.07: 20 7.07 - 8.84: 4 Bond angle restraints: 5584 Sorted by residual: angle pdb=" C TYR A 113 " pdb=" CA TYR A 113 " pdb=" CB TYR A 113 " ideal model delta sigma weight residual 110.88 102.05 8.83 1.57e+00 4.06e-01 3.17e+01 angle pdb=" N ILE B 142 " pdb=" CA ILE B 142 " pdb=" C ILE B 142 " ideal model delta sigma weight residual 108.12 114.95 -6.83 1.34e+00 5.57e-01 2.59e+01 angle pdb=" C THR B 28 " pdb=" CA THR B 28 " pdb=" CB THR B 28 " ideal model delta sigma weight residual 109.51 117.98 -8.47 1.71e+00 3.42e-01 2.46e+01 angle pdb=" N VAL B 50 " pdb=" CA VAL B 50 " pdb=" C VAL B 50 " ideal model delta sigma weight residual 109.30 115.19 -5.89 1.25e+00 6.40e-01 2.22e+01 angle pdb=" N LEU B 101 " pdb=" CA LEU B 101 " pdb=" C LEU B 101 " ideal model delta sigma weight residual 110.48 103.68 6.80 1.48e+00 4.57e-01 2.11e+01 ... (remaining 5579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 2073 17.02 - 34.04: 190 34.04 - 51.07: 41 51.07 - 68.09: 13 68.09 - 85.11: 4 Dihedral angle restraints: 2321 sinusoidal: 661 harmonic: 1660 Sorted by residual: dihedral pdb=" CA PRO A 348 " pdb=" C PRO A 348 " pdb=" N LEU A 349 " pdb=" CA LEU A 349 " ideal model delta harmonic sigma weight residual 180.00 140.49 39.51 0 5.00e+00 4.00e-02 6.24e+01 dihedral pdb=" C VAL B 50 " pdb=" N VAL B 50 " pdb=" CA VAL B 50 " pdb=" CB VAL B 50 " ideal model delta harmonic sigma weight residual -122.00 -139.11 17.11 0 2.50e+00 1.60e-01 4.68e+01 dihedral pdb=" N VAL B 50 " pdb=" C VAL B 50 " pdb=" CA VAL B 50 " pdb=" CB VAL B 50 " ideal model delta harmonic sigma weight residual 123.40 139.16 -15.76 0 2.50e+00 1.60e-01 3.97e+01 ... (remaining 2318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 580 0.112 - 0.224: 62 0.224 - 0.337: 10 0.337 - 0.449: 6 0.449 - 0.561: 3 Chirality restraints: 661 Sorted by residual: chirality pdb=" CA VAL B 50 " pdb=" N VAL B 50 " pdb=" C VAL B 50 " pdb=" CB VAL B 50 " both_signs ideal model delta sigma weight residual False 2.44 1.88 0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" CA GLU B 172 " pdb=" N GLU B 172 " pdb=" C GLU B 172 " pdb=" CB GLU B 172 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.78e+00 chirality pdb=" CA GLU B 155 " pdb=" N GLU B 155 " pdb=" C GLU B 155 " pdb=" CB GLU B 155 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.73e+00 ... (remaining 658 not shown) Planarity restraints: 715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 103 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.50e+00 pdb=" C GLY B 103 " -0.044 2.00e-02 2.50e+03 pdb=" O GLY B 103 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO B 104 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 27 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C PHE A 27 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE A 27 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE A 28 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 347 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO A 348 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 348 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 348 " 0.030 5.00e-02 4.00e+02 ... (remaining 712 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 108 2.68 - 3.24: 4150 3.24 - 3.79: 5870 3.79 - 4.35: 7286 4.35 - 4.90: 11766 Nonbonded interactions: 29180 Sorted by model distance: nonbonded pdb=" O GLN A 291 " pdb=" ND1 HIS A 292 " model vdw 2.126 3.120 nonbonded pdb=" O THR A 352 " pdb=" N GLY A 355 " model vdw 2.212 3.120 nonbonded pdb=" OG1 THR A 108 " pdb=" OE1 GLN A 111 " model vdw 2.227 3.040 nonbonded pdb=" O LYS A 297 " pdb=" OH TYR A 353 " model vdw 2.248 3.040 nonbonded pdb=" O VAL B 221 " pdb=" OG1 THR B 224 " model vdw 2.293 3.040 ... (remaining 29175 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.620 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.320 Find NCS groups from input model: 0.020 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 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 : 0.008 0.042 4091 Z= 0.554 Angle : 1.172 8.839 5584 Z= 0.795 Chirality : 0.088 0.561 661 Planarity : 0.005 0.054 715 Dihedral : 15.050 85.110 1267 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.11 % Favored : 88.72 % Rotamer: Outliers : 5.25 % Allowed : 10.49 % Favored : 84.26 % Cbeta Deviations : 1.90 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.02 (0.29), residues: 585 helix: -2.79 (0.21), residues: 333 sheet: 0.27 (0.53), residues: 94 loop : -3.79 (0.39), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 328 TYR 0.016 0.001 TYR A 113 PHE 0.014 0.002 PHE A 332 TRP 0.020 0.001 TRP A 424 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00830 / 0.55 ( 4091) covalent geometry : angle 1.17212 / 0.79 ( 5584) hydrogen bonds : bond 0.14664 / 9.03 ( 281) hydrogen bonds : angle 7.64240 / 5.57 ( 819) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.190 Fit side-chains REVERT: A 60 TRP cc_start: 0.6388 (OUTLIER) cc_final: 0.5670 (m-10) REVERT: A 111 GLN cc_start: 0.6960 (OUTLIER) cc_final: 0.6646 (mt0) REVERT: A 196 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7670 (mtm180) REVERT: A 388 SER cc_start: 0.7609 (OUTLIER) cc_final: 0.7390 (p) REVERT: A 416 TYR cc_start: 0.5679 (m-80) cc_final: 0.5117 (m-80) REVERT: A 438 PHE cc_start: 0.7251 (t80) cc_final: 0.6994 (t80) outliers start: 17 outliers final: 4 residues processed: 106 average time/residue: 0.0554 time to fit residues: 7.7170 Evaluate side-chains 79 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 115 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 40.0000 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 30.0000 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 ASN A 165 ASN A 260 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.226846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.183414 restraints weight = 5494.509| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 3.40 r_work: 0.4125 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4091 Z= 0.158 Angle : 0.719 8.248 5584 Z= 0.373 Chirality : 0.044 0.146 661 Planarity : 0.005 0.065 715 Dihedral : 7.196 57.199 637 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.32 % Allowed : 20.37 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.44 (0.34), residues: 585 helix: -0.57 (0.28), residues: 334 sheet: 1.14 (0.55), residues: 95 loop : -3.01 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 203 TYR 0.022 0.002 TYR A 113 PHE 0.052 0.002 PHE A 332 TRP 0.011 0.001 TRP A 424 HIS 0.002 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 4091) covalent geometry : angle 0.71891 / 0.37 ( 5584) hydrogen bonds : bond 0.04721 / 3.13 ( 281) hydrogen bonds : angle 5.05731 / 3.68 ( 819) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.172 Fit side-chains REVERT: B 203 ARG cc_start: 0.6107 (mtm110) cc_final: 0.5809 (mtp-110) outliers start: 14 outliers final: 10 residues processed: 95 average time/residue: 0.0530 time to fit residues: 6.6885 Evaluate side-chains 85 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 221 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 43 optimal weight: 50.0000 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 30.0000 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 50.0000 chunk 57 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4747 r_free = 0.4747 target = 0.229615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.185629 restraints weight = 5488.215| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 3.48 r_work: 0.4068 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4091 Z= 0.143 Angle : 0.665 6.883 5584 Z= 0.343 Chirality : 0.043 0.144 661 Planarity : 0.004 0.064 715 Dihedral : 5.322 52.349 624 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.40 % Allowed : 25.93 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.60 (0.36), residues: 585 helix: 0.07 (0.29), residues: 341 sheet: 0.94 (0.50), residues: 111 loop : -2.60 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 196 TYR 0.016 0.001 TYR A 113 PHE 0.010 0.001 PHE A 27 TRP 0.014 0.002 TRP A 174 HIS 0.002 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 4091) covalent geometry : angle 0.66462 / 0.34 ( 5584) hydrogen bonds : bond 0.04283 / 2.81 ( 281) hydrogen bonds : angle 4.51426 / 3.26 ( 819) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 151 MET cc_start: 0.7768 (mmm) cc_final: 0.7459 (mmm) REVERT: A 322 THR cc_start: 0.8498 (t) cc_final: 0.8228 (p) REVERT: A 371 SER cc_start: 0.9078 (m) cc_final: 0.8403 (p) REVERT: A 411 ARG cc_start: 0.6439 (ttt-90) cc_final: 0.4542 (ttp-170) outliers start: 11 outliers final: 10 residues processed: 98 average time/residue: 0.0615 time to fit residues: 7.7562 Evaluate side-chains 87 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 221 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 0.0060 chunk 44 optimal weight: 40.0000 chunk 49 optimal weight: 20.0000 chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.4759 r_free = 0.4759 target = 0.230845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.186651 restraints weight = 5549.323| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 3.61 r_work: 0.4098 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4091 Z= 0.128 Angle : 0.638 8.177 5584 Z= 0.329 Chirality : 0.042 0.136 661 Planarity : 0.004 0.064 715 Dihedral : 5.184 50.329 624 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 6.17 % Allowed : 24.38 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.36), residues: 585 helix: 0.50 (0.29), residues: 340 sheet: 1.05 (0.50), residues: 111 loop : -2.65 (0.52), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 203 TYR 0.014 0.001 TYR A 113 PHE 0.019 0.001 PHE A 274 TRP 0.019 0.002 TRP A 18 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 4091) covalent geometry : angle 0.63848 / 0.33 ( 5584) hydrogen bonds : bond 0.03918 / 2.57 ( 281) hydrogen bonds : angle 4.35943 / 3.15 ( 819) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.135 Fit side-chains REVERT: A 149 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7736 (mp) REVERT: A 151 MET cc_start: 0.7815 (mmm) cc_final: 0.7524 (mmm) REVERT: A 345 MET cc_start: 0.6806 (tmm) cc_final: 0.6328 (tmm) REVERT: A 371 SER cc_start: 0.8980 (m) cc_final: 0.8122 (p) REVERT: A 378 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7894 (tt) REVERT: A 395 THR cc_start: 0.7770 (m) cc_final: 0.7563 (m) REVERT: A 411 ARG cc_start: 0.6429 (ttt-90) cc_final: 0.4418 (ttp-170) outliers start: 20 outliers final: 13 residues processed: 98 average time/residue: 0.0561 time to fit residues: 7.1856 Evaluate side-chains 95 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 221 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 43 optimal weight: 50.0000 chunk 41 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 ASN A 292 HIS ** A 330 GLN ** 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 = 0.4676 r_free = 0.4676 target = 0.221105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.175349 restraints weight = 5573.774| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 3.50 r_work: 0.3993 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4091 Z= 0.176 Angle : 0.716 11.851 5584 Z= 0.361 Chirality : 0.044 0.160 661 Planarity : 0.004 0.063 715 Dihedral : 5.360 53.181 624 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 8.95 % Allowed : 23.77 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.10 (0.36), residues: 585 helix: 0.51 (0.29), residues: 340 sheet: 1.26 (0.51), residues: 109 loop : -2.59 (0.52), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 313 TYR 0.016 0.001 TYR A 138 PHE 0.042 0.002 PHE A 332 TRP 0.032 0.003 TRP A 174 HIS 0.014 0.002 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 ( 4091) covalent geometry : angle 0.71643 / 0.36 ( 5584) hydrogen bonds : bond 0.04742 / 3.17 ( 281) hydrogen bonds : angle 4.44524 / 3.20 ( 819) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 149 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7887 (mp) REVERT: A 293 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.6167 (m-10) REVERT: A 302 LEU cc_start: 0.8097 (mm) cc_final: 0.7832 (mt) REVERT: A 345 MET cc_start: 0.6800 (tmm) cc_final: 0.6543 (tmm) REVERT: A 378 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8019 (tt) REVERT: A 415 MET cc_start: 0.7625 (mmm) cc_final: 0.7401 (mmt) REVERT: B 203 ARG cc_start: 0.6497 (mtp-110) cc_final: 0.6261 (mtm180) outliers start: 29 outliers final: 24 residues processed: 95 average time/residue: 0.0505 time to fit residues: 6.3272 Evaluate side-chains 101 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 221 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.5980 chunk 40 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 2 optimal weight: 0.0170 chunk 41 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 overall best weight: 1.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 GLN ** 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 = 0.4638 r_free = 0.4638 target = 0.219992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.177546 restraints weight = 5859.236| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 3.57 r_work: 0.4164 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4091 Z= 0.157 Angle : 0.700 11.916 5584 Z= 0.346 Chirality : 0.043 0.150 661 Planarity : 0.004 0.063 715 Dihedral : 5.281 51.914 624 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 9.26 % Allowed : 26.54 % Favored : 64.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.13 (0.36), residues: 585 helix: 0.69 (0.29), residues: 340 sheet: 1.41 (0.51), residues: 109 loop : -2.56 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 313 TYR 0.012 0.001 TYR A 138 PHE 0.041 0.002 PHE A 332 TRP 0.026 0.002 TRP A 174 HIS 0.002 0.001 HIS B 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 4091) covalent geometry : angle 0.70017 / 0.35 ( 5584) hydrogen bonds : bond 0.04478 / 2.98 ( 281) hydrogen bonds : angle 4.34941 / 3.13 ( 819) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.091 Fit side-chains REVERT: A 293 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.6229 (m-10) REVERT: A 345 MET cc_start: 0.6937 (tmm) cc_final: 0.6684 (tmm) REVERT: A 378 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8293 (tt) REVERT: A 419 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.7132 (t80) REVERT: A 446 ARG cc_start: 0.7446 (tpt170) cc_final: 0.7162 (ttt180) REVERT: B 203 ARG cc_start: 0.6655 (mtp-110) cc_final: 0.6453 (mtm180) outliers start: 30 outliers final: 22 residues processed: 99 average time/residue: 0.0546 time to fit residues: 6.9117 Evaluate side-chains 104 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 221 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 50.0000 chunk 46 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.0570 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.220500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.178631 restraints weight = 5733.828| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 3.61 r_work: 0.4170 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4091 Z= 0.134 Angle : 0.670 12.122 5584 Z= 0.329 Chirality : 0.042 0.138 661 Planarity : 0.004 0.062 715 Dihedral : 5.239 53.676 624 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 9.88 % Allowed : 26.23 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.37), residues: 585 helix: 0.93 (0.30), residues: 341 sheet: 1.51 (0.52), residues: 109 loop : -2.38 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 446 TYR 0.011 0.001 TYR A 113 PHE 0.041 0.002 PHE A 332 TRP 0.021 0.002 TRP A 174 HIS 0.001 0.000 HIS B 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 4091) covalent geometry : angle 0.66950 / 0.33 ( 5584) hydrogen bonds : bond 0.04093 / 2.72 ( 281) hydrogen bonds : angle 4.18985 / 3.02 ( 819) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: A 149 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7867 (mp) REVERT: A 302 LEU cc_start: 0.8012 (mm) cc_final: 0.7691 (mp) REVERT: A 345 MET cc_start: 0.6700 (tmm) cc_final: 0.6479 (tmm) REVERT: A 378 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8160 (tt) REVERT: A 419 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.6932 (t80) REVERT: A 446 ARG cc_start: 0.7540 (tpt170) cc_final: 0.7109 (ttt180) REVERT: B 203 ARG cc_start: 0.6653 (mtp-110) cc_final: 0.6342 (mtm180) outliers start: 32 outliers final: 23 residues processed: 103 average time/residue: 0.0514 time to fit residues: 6.9884 Evaluate side-chains 104 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 221 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 53 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 45 optimal weight: 50.0000 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 40.0000 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 48 optimal weight: 30.0000 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN ** A 330 GLN ** 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 = 0.4643 r_free = 0.4643 target = 0.221766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.180147 restraints weight = 5657.531| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 3.56 r_work: 0.4181 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4091 Z= 0.132 Angle : 0.669 11.836 5584 Z= 0.331 Chirality : 0.042 0.139 661 Planarity : 0.004 0.062 715 Dihedral : 5.176 53.592 624 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 7.72 % Allowed : 29.94 % Favored : 62.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.59 (0.37), residues: 585 helix: 1.08 (0.30), residues: 340 sheet: 1.63 (0.52), residues: 109 loop : -2.46 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 261 TYR 0.011 0.001 TYR A 113 PHE 0.043 0.002 PHE A 332 TRP 0.020 0.002 TRP A 18 HIS 0.001 0.000 HIS B 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 4091) covalent geometry : angle 0.66895 / 0.33 ( 5584) hydrogen bonds : bond 0.03994 / 2.65 ( 281) hydrogen bonds : angle 4.14199 / 2.98 ( 819) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 151 MET cc_start: 0.7733 (mmm) cc_final: 0.7400 (mmm) REVERT: A 345 MET cc_start: 0.6681 (tmm) cc_final: 0.6458 (tmm) REVERT: A 378 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8148 (tt) REVERT: A 419 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.6866 (t80) REVERT: A 446 ARG cc_start: 0.7434 (tpt170) cc_final: 0.7050 (ttt180) outliers start: 25 outliers final: 23 residues processed: 94 average time/residue: 0.0543 time to fit residues: 6.6109 Evaluate side-chains 103 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 221 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 50 optimal weight: 0.0970 chunk 42 optimal weight: 20.0000 chunk 43 optimal weight: 50.0000 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 30.0000 chunk 54 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN A 165 ASN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.219107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.177182 restraints weight = 5798.519| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 3.56 r_work: 0.4161 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4091 Z= 0.146 Angle : 0.679 11.918 5584 Z= 0.337 Chirality : 0.043 0.135 661 Planarity : 0.004 0.062 715 Dihedral : 5.058 49.150 624 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 9.26 % Allowed : 27.16 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.61 (0.37), residues: 585 helix: 1.03 (0.29), residues: 340 sheet: 1.88 (0.52), residues: 107 loop : -2.43 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 203 TYR 0.011 0.001 TYR A 113 PHE 0.044 0.002 PHE A 332 TRP 0.027 0.002 TRP A 18 HIS 0.001 0.000 HIS B 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 4091) covalent geometry : angle 0.67884 / 0.34 ( 5584) hydrogen bonds : bond 0.04202 / 2.81 ( 281) hydrogen bonds : angle 4.17721 / 3.01 ( 819) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 149 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7895 (mp) REVERT: A 302 LEU cc_start: 0.8111 (mm) cc_final: 0.7903 (mt) REVERT: A 345 MET cc_start: 0.6727 (tmm) cc_final: 0.6252 (tmm) REVERT: A 378 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8231 (tt) REVERT: A 393 LEU cc_start: 0.8292 (mp) cc_final: 0.8089 (mp) REVERT: A 419 TYR cc_start: 0.8397 (OUTLIER) cc_final: 0.6904 (t80) REVERT: A 446 ARG cc_start: 0.7514 (tpt170) cc_final: 0.7127 (ttt180) outliers start: 30 outliers final: 24 residues processed: 100 average time/residue: 0.0445 time to fit residues: 6.0563 Evaluate side-chains 105 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 0.0870 chunk 39 optimal weight: 20.0000 chunk 5 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 47 optimal weight: 20.0000 chunk 13 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN A 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.222550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.180897 restraints weight = 5658.646| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 3.56 r_work: 0.4173 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4091 Z= 0.125 Angle : 0.677 11.905 5584 Z= 0.330 Chirality : 0.042 0.122 661 Planarity : 0.004 0.062 715 Dihedral : 5.046 49.602 624 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 7.72 % Allowed : 29.32 % Favored : 62.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.82 (0.37), residues: 585 helix: 1.21 (0.30), residues: 338 sheet: 1.97 (0.52), residues: 107 loop : -2.34 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 261 TYR 0.010 0.001 TYR A 113 PHE 0.045 0.002 PHE A 332 TRP 0.022 0.002 TRP A 18 HIS 0.001 0.000 HIS B 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 4091) covalent geometry : angle 0.67717 / 0.33 ( 5584) hydrogen bonds : bond 0.03876 / 2.57 ( 281) hydrogen bonds : angle 4.08296 / 2.94 ( 819) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: A 149 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7831 (mp) REVERT: A 151 MET cc_start: 0.7655 (mmm) cc_final: 0.7326 (mmm) REVERT: A 302 LEU cc_start: 0.8029 (mm) cc_final: 0.7722 (mp) REVERT: A 345 MET cc_start: 0.6592 (tmm) cc_final: 0.6109 (tmm) REVERT: A 378 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8105 (tt) REVERT: A 393 LEU cc_start: 0.8247 (mp) cc_final: 0.8008 (mp) REVERT: A 419 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.6723 (t80) REVERT: A 446 ARG cc_start: 0.7510 (tpt170) cc_final: 0.7095 (ttt180) outliers start: 25 outliers final: 21 residues processed: 92 average time/residue: 0.0438 time to fit residues: 5.4174 Evaluate side-chains 101 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 49 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 20 optimal weight: 0.1980 chunk 34 optimal weight: 0.0980 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 30.0000 chunk 56 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN A 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.221648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.179480 restraints weight = 5756.455| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 3.60 r_work: 0.4159 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4091 Z= 0.133 Angle : 0.689 12.069 5584 Z= 0.335 Chirality : 0.042 0.131 661 Planarity : 0.004 0.061 715 Dihedral : 5.031 49.426 624 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 8.02 % Allowed : 29.63 % Favored : 62.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.83 (0.37), residues: 585 helix: 1.22 (0.30), residues: 338 sheet: 2.00 (0.52), residues: 107 loop : -2.35 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 261 TYR 0.011 0.001 TYR A 113 PHE 0.044 0.002 PHE A 332 TRP 0.030 0.002 TRP A 18 HIS 0.001 0.000 HIS B 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 4091) covalent geometry : angle 0.68888 / 0.33 ( 5584) hydrogen bonds : bond 0.03961 / 2.64 ( 281) hydrogen bonds : angle 4.10414 / 2.96 ( 819) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1015.25 seconds wall clock time: 18 minutes 20.57 seconds (1100.57 seconds total)