Starting phenix.real_space_refine on Fri Aug 22 14:21:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lz0_30020/08_2025/6lz0_30020.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lz0_30020/08_2025/6lz0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6lz0_30020/08_2025/6lz0_30020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lz0_30020/08_2025/6lz0_30020.map" model { file = "/net/cci-nas-00/data/ceres_data/6lz0_30020/08_2025/6lz0_30020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lz0_30020/08_2025/6lz0_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 1.53, per 1000 atoms: 0.38 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: 0.40 Conformation dependent library (CDL) restraints added in 209.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.43 Time building geometry restraints manager: 0.52 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: 193 34.04 - 51.07: 42 51.07 - 68.09: 13 68.09 - 85.11: 4 Dihedral angle restraints: 2325 sinusoidal: 665 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 2322 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: 0.690 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: 6.370 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5972 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 : 15.109 85.110 1271 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 aren 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 covalent geometry : bond 0.00830 ( 4091) covalent geometry : angle 1.17212 ( 5584) hydrogen bonds : bond 0.14664 ( 281) hydrogen bonds : angle 7.64240 ( 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 : 0.140 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: 0.7669 (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: 0.0588 time to fit residues: 8.0679 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 : 0.142 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.227378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.181973 restraints weight = 5685.392| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 3.63 r_work: 0.4121 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.2767 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= 0.159 Angle : 0.716 8.163 5584 Z= 0.372 Chirality : 0.044 0.151 661 Planarity : 0.005 0.065 715 Dihedral : 7.593 57.210 641 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.70 % Allowed : 21.60 % Favored : 74.69 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -1.49 (0.34), residues: 585 helix: -0.61 (0.28), residues: 334 sheet: 1.12 (0.54), residues: 95 loop : -3.04 (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 covalent geometry : bond 0.00343 ( 4091) covalent geometry : angle 0.71581 ( 5584) hydrogen bonds : bond 0.04822 ( 281) hydrogen bonds : angle 5.06966 ( 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 98 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.140 Fit side-chains REVERT: A 287 TYR cc_start: 0.8122 (t80) cc_final: 0.7720 (t80) outliers start: 12 outliers final: 9 residues processed: 95 average time/residue: 0.0558 time to fit residues: 6.9319 Evaluate side-chains 83 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 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 94 CYS 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: 0.5980 chunk 6 optimal weight: 0.0770 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 30.0000 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 30.0000 chunk 57 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 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 = 0.4773 r_free = 0.4773 target = 0.233265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.189727 restraints weight = 5553.165| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 3.62 r_work: 0.4114 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.3641 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= 0.133 Angle : 0.657 8.362 5584 Z= 0.338 Chirality : 0.042 0.131 661 Planarity : 0.005 0.064 715 Dihedral : 5.849 53.265 628 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 5.25 % Allowed : 23.15 % Favored : 71.60 % 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 aren not related in a simple way. whole: -0.52 (0.36), residues: 585 helix: 0.19 (0.29), residues: 339 sheet: 0.91 (0.50), residues: 111 loop : -2.65 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 196 TYR 0.017 0.001 TYR A 113 PHE 0.011 0.001 PHE A 332 TRP 0.012 0.001 TRP A 174 HIS 0.003 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4091) covalent geometry : angle 0.65716 ( 5584) hydrogen bonds : bond 0.04083 ( 281) hydrogen bonds : angle 4.47147 ( 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 103 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 151 MET cc_start: 0.7607 (mmm) cc_final: 0.7225 (mmm) REVERT: A 277 LEU cc_start: 0.8129 (tp) cc_final: 0.7562 (tt) REVERT: A 329 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7560 (tt) REVERT: A 371 SER cc_start: 0.9074 (m) cc_final: 0.8319 (p) REVERT: A 411 ARG cc_start: 0.6371 (ttt-90) cc_final: 0.4516 (ttp-170) REVERT: B 203 ARG cc_start: 0.6499 (mtp-110) cc_final: 0.5465 (mtm180) outliers start: 17 outliers final: 12 residues processed: 95 average time/residue: 0.0664 time to fit residues: 8.0603 Evaluate side-chains 91 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 TYR 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 127 ASN Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 CYS 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: 3.9990 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 44 optimal weight: 50.0000 chunk 49 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 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 = 0.4767 r_free = 0.4767 target = 0.231156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.186789 restraints weight = 5460.330| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 3.53 r_work: 0.4106 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4091 Z= 0.134 Angle : 0.657 7.681 5584 Z= 0.334 Chirality : 0.042 0.162 661 Planarity : 0.004 0.062 715 Dihedral : 5.859 51.328 628 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 6.48 % Allowed : 24.07 % 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 aren not related in a simple way. whole: -0.20 (0.36), residues: 585 helix: 0.45 (0.29), residues: 341 sheet: 1.04 (0.50), residues: 111 loop : -2.61 (0.52), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 203 TYR 0.013 0.001 TYR A 113 PHE 0.011 0.001 PHE A 332 TRP 0.027 0.002 TRP A 18 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 4091) covalent geometry : angle 0.65657 ( 5584) hydrogen bonds : bond 0.04046 ( 281) hydrogen bonds : angle 4.36410 ( 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 108 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: A 149 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7769 (mp) REVERT: A 151 MET cc_start: 0.7875 (mmm) cc_final: 0.7528 (mmm) REVERT: A 273 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7290 (ttm) REVERT: A 411 ARG cc_start: 0.6500 (ttt-90) cc_final: 0.4508 (ttp-170) REVERT: A 415 MET cc_start: 0.7748 (mmm) cc_final: 0.7475 (mmt) REVERT: B 203 ARG cc_start: 0.6608 (mtp-110) cc_final: 0.6191 (mtm180) outliers start: 21 outliers final: 12 residues processed: 97 average time/residue: 0.0675 time to fit residues: 8.2123 Evaluate side-chains 92 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 109 VAL 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 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 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: 3.9990 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 54 optimal weight: 40.0000 chunk 46 optimal weight: 10.0000 chunk 47 optimal weight: 50.0000 chunk 43 optimal weight: 50.0000 chunk 41 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 292 HIS ** 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 = 0.4648 r_free = 0.4648 target = 0.220968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.177418 restraints weight = 5705.351| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 3.58 r_work: 0.4166 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4091 Z= 0.169 Angle : 0.721 11.827 5584 Z= 0.366 Chirality : 0.045 0.154 661 Planarity : 0.004 0.062 715 Dihedral : 5.914 50.682 628 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 8.64 % Allowed : 26.85 % Favored : 64.51 % 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 aren not related in a simple way. whole: -0.18 (0.36), residues: 585 helix: 0.44 (0.29), residues: 340 sheet: 1.25 (0.49), residues: 111 loop : -2.71 (0.51), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 196 TYR 0.016 0.001 TYR A 138 PHE 0.014 0.001 PHE A 274 TRP 0.030 0.003 TRP A 174 HIS 0.014 0.002 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 4091) covalent geometry : angle 0.72077 ( 5584) hydrogen bonds : bond 0.04810 ( 281) hydrogen bonds : angle 4.45546 ( 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 109 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 149 LEU cc_start: 0.8321 (mm) cc_final: 0.7933 (mp) REVERT: A 293 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.6212 (m-10) REVERT: A 345 MET cc_start: 0.6907 (tmm) cc_final: 0.6496 (tmm) REVERT: A 371 SER cc_start: 0.8986 (m) cc_final: 0.8059 (p) REVERT: A 378 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8179 (tt) REVERT: A 393 LEU cc_start: 0.8328 (mp) cc_final: 0.8127 (mp) REVERT: A 415 MET cc_start: 0.7786 (mmm) cc_final: 0.7561 (mmt) REVERT: B 203 ARG cc_start: 0.6630 (mtp-110) cc_final: 0.6148 (mtm180) outliers start: 28 outliers final: 20 residues processed: 101 average time/residue: 0.0550 time to fit residues: 7.3229 Evaluate side-chains 97 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 100 LEU 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 189 CYS Chi-restraints excluded: chain A residue 190 VAL 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 378 LEU 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: 0.7980 chunk 40 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 41 optimal weight: 50.0000 chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 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 = 0.4659 r_free = 0.4659 target = 0.222768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.179440 restraints weight = 5897.794| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 3.70 r_work: 0.4129 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.4986 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 : 0.689 11.528 5584 Z= 0.342 Chirality : 0.042 0.144 661 Planarity : 0.004 0.062 715 Dihedral : 5.853 48.579 628 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 8.64 % Allowed : 29.32 % Favored : 62.04 % 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 aren not related in a simple way. whole: 0.13 (0.36), residues: 585 helix: 0.67 (0.29), residues: 340 sheet: 1.39 (0.49), residues: 111 loop : -2.53 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 446 TYR 0.013 0.001 TYR A 113 PHE 0.040 0.001 PHE A 332 TRP 0.023 0.002 TRP A 174 HIS 0.002 0.000 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4091) covalent geometry : angle 0.68944 ( 5584) hydrogen bonds : bond 0.04271 ( 281) hydrogen bonds : angle 4.33175 ( 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 105 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 149 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7921 (mp) REVERT: A 323 LYS cc_start: 0.8264 (tttt) cc_final: 0.7673 (tmmt) REVERT: A 345 MET cc_start: 0.6870 (tmm) cc_final: 0.6634 (tmm) REVERT: A 378 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8148 (tt) REVERT: A 446 ARG cc_start: 0.7509 (tpt170) cc_final: 0.7133 (ttt180) REVERT: B 203 ARG cc_start: 0.6648 (mtp-110) cc_final: 0.6158 (mtm180) outliers start: 28 outliers final: 19 residues processed: 96 average time/residue: 0.0583 time to fit residues: 7.3301 Evaluate side-chains 94 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 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 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 408 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 50.0000 chunk 46 optimal weight: 30.0000 chunk 52 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.0040 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.221806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.180462 restraints weight = 5685.924| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 3.50 r_work: 0.4164 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4091 Z= 0.141 Angle : 0.683 11.457 5584 Z= 0.338 Chirality : 0.043 0.141 661 Planarity : 0.004 0.062 715 Dihedral : 5.801 47.896 628 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 8.33 % Allowed : 29.01 % Favored : 62.65 % 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 aren not related in a simple way. whole: 0.29 (0.36), residues: 585 helix: 0.76 (0.29), residues: 341 sheet: 1.52 (0.50), residues: 111 loop : -2.44 (0.52), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 196 TYR 0.012 0.001 TYR A 113 PHE 0.042 0.002 PHE A 332 TRP 0.025 0.002 TRP A 18 HIS 0.001 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 4091) covalent geometry : angle 0.68323 ( 5584) hydrogen bonds : bond 0.04204 ( 281) hydrogen bonds : angle 4.22924 ( 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 106 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.145 Fit side-chains REVERT: A 149 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7884 (mp) REVERT: A 316 MET cc_start: 0.8395 (mmt) cc_final: 0.8150 (mmt) REVERT: A 319 VAL cc_start: 0.8217 (t) cc_final: 0.7954 (p) REVERT: A 323 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7661 (tmmt) REVERT: A 345 MET cc_start: 0.6800 (tmm) cc_final: 0.6311 (tmm) REVERT: A 378 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8247 (tt) REVERT: A 393 LEU cc_start: 0.8391 (mp) cc_final: 0.8185 (mp) REVERT: A 446 ARG cc_start: 0.7518 (tpt170) cc_final: 0.7084 (ttt180) REVERT: B 203 ARG cc_start: 0.6624 (mtp-110) cc_final: 0.6185 (mtm180) outliers start: 27 outliers final: 21 residues processed: 94 average time/residue: 0.0559 time to fit residues: 6.8408 Evaluate side-chains 96 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.138 ------------------------------------------------------------------------------- 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 109 VAL 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 164 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 323 LYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 408 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 53 optimal weight: 30.0000 chunk 3 optimal weight: 7.9990 chunk 45 optimal weight: 50.0000 chunk 36 optimal weight: 0.5980 chunk 52 optimal weight: 40.0000 chunk 34 optimal weight: 0.0570 chunk 19 optimal weight: 4.9990 chunk 48 optimal weight: 50.0000 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 270 ASN ** 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 = 0.4657 r_free = 0.4657 target = 0.222759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.180369 restraints weight = 5702.814| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 3.60 r_work: 0.4137 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.5394 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= 0.137 Angle : 0.683 10.827 5584 Z= 0.337 Chirality : 0.043 0.253 661 Planarity : 0.004 0.062 715 Dihedral : 5.805 47.941 628 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 7.41 % Allowed : 30.56 % Favored : 62.04 % 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 aren not related in a simple way. whole: 0.46 (0.37), residues: 585 helix: 0.90 (0.29), residues: 340 sheet: 1.68 (0.50), residues: 111 loop : -2.43 (0.52), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 261 TYR 0.011 0.001 TYR A 113 PHE 0.043 0.002 PHE A 332 TRP 0.025 0.002 TRP A 18 HIS 0.001 0.000 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4091) covalent geometry : angle 0.68282 ( 5584) hydrogen bonds : bond 0.04068 ( 281) hydrogen bonds : angle 4.17826 ( 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 97 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: A 149 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7869 (mp) REVERT: A 319 VAL cc_start: 0.8212 (t) cc_final: 0.7947 (p) REVERT: A 323 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7643 (tmmt) REVERT: A 345 MET cc_start: 0.6754 (tmm) cc_final: 0.6272 (tmm) REVERT: A 378 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8141 (tt) REVERT: A 419 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.6730 (t80) REVERT: A 446 ARG cc_start: 0.7443 (tpt170) cc_final: 0.7046 (ttt180) REVERT: B 203 ARG cc_start: 0.6612 (mtp-110) cc_final: 0.6174 (mtm180) outliers start: 24 outliers final: 18 residues processed: 89 average time/residue: 0.0550 time to fit residues: 6.5688 Evaluate side-chains 93 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 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 189 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 286 SER 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 371 SER Chi-restraints excluded: chain A residue 378 LEU 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: 20.0000 chunk 42 optimal weight: 7.9990 chunk 43 optimal weight: 50.0000 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 37 optimal weight: 30.0000 chunk 54 optimal weight: 30.0000 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 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 = 0.4601 r_free = 0.4601 target = 0.215829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.172507 restraints weight = 5853.330| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 3.54 r_work: 0.4012 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4091 Z= 0.201 Angle : 0.760 10.849 5584 Z= 0.383 Chirality : 0.047 0.267 661 Planarity : 0.005 0.064 715 Dihedral : 5.953 47.610 628 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 8.64 % Allowed : 28.70 % Favored : 62.65 % 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 aren not related in a simple way. whole: 0.23 (0.36), residues: 585 helix: 0.61 (0.29), residues: 338 sheet: 1.85 (0.50), residues: 109 loop : -2.39 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 261 TYR 0.017 0.002 TYR A 138 PHE 0.045 0.002 PHE A 332 TRP 0.040 0.003 TRP A 18 HIS 0.002 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 4091) covalent geometry : angle 0.76032 ( 5584) hydrogen bonds : bond 0.05092 ( 281) hydrogen bonds : angle 4.45769 ( 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 109 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.144 Fit side-chains REVERT: A 149 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7970 (mp) REVERT: A 302 LEU cc_start: 0.8009 (mm) cc_final: 0.7731 (mp) REVERT: A 307 PHE cc_start: 0.7416 (t80) cc_final: 0.7172 (t80) REVERT: A 316 MET cc_start: 0.8476 (mmt) cc_final: 0.8165 (mmt) REVERT: A 319 VAL cc_start: 0.8231 (t) cc_final: 0.7964 (p) REVERT: A 323 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7228 (pttm) REVERT: A 345 MET cc_start: 0.6957 (tmm) cc_final: 0.6470 (tmm) REVERT: A 378 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8230 (tt) REVERT: A 379 MET cc_start: 0.7986 (mpp) cc_final: 0.7758 (mpp) REVERT: A 393 LEU cc_start: 0.8128 (mp) cc_final: 0.7904 (mp) REVERT: A 419 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.6844 (t80) REVERT: A 446 ARG cc_start: 0.7614 (tpt170) cc_final: 0.7160 (ttt180) REVERT: B 203 ARG cc_start: 0.6754 (mtp-110) cc_final: 0.6334 (mtm180) outliers start: 28 outliers final: 21 residues processed: 101 average time/residue: 0.0519 time to fit residues: 7.0653 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 : 0.146 ------------------------------------------------------------------------------- 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 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 189 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 295 SER 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 371 SER Chi-restraints excluded: chain A residue 378 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 6 optimal weight: 0.0770 chunk 39 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 40.0000 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 47 optimal weight: 40.0000 chunk 13 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.223103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.180943 restraints weight = 5712.734| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 3.59 r_work: 0.4150 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.5709 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 : 0.687 10.756 5584 Z= 0.340 Chirality : 0.044 0.277 661 Planarity : 0.004 0.061 715 Dihedral : 5.790 47.639 628 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.56 % Allowed : 32.72 % Favored : 61.73 % 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 aren not related in a simple way. whole: 0.58 (0.37), residues: 585 helix: 0.94 (0.30), residues: 338 sheet: 1.92 (0.51), residues: 109 loop : -2.33 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 261 TYR 0.013 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 covalent geometry : bond 0.00286 ( 4091) covalent geometry : angle 0.68742 ( 5584) hydrogen bonds : bond 0.04030 ( 281) hydrogen bonds : angle 4.15236 ( 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 95 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.245 Fit side-chains REVERT: A 149 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7912 (mp) REVERT: A 307 PHE cc_start: 0.7466 (t80) cc_final: 0.7237 (t80) REVERT: A 316 MET cc_start: 0.8384 (mmt) cc_final: 0.8103 (mmt) REVERT: A 319 VAL cc_start: 0.8205 (t) cc_final: 0.7931 (p) REVERT: A 323 LYS cc_start: 0.8129 (tttt) cc_final: 0.7317 (pttm) REVERT: A 345 MET cc_start: 0.6652 (tmm) cc_final: 0.6205 (tmm) REVERT: A 378 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8171 (tt) REVERT: A 393 LEU cc_start: 0.8082 (mp) cc_final: 0.7843 (mp) REVERT: A 419 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.6825 (t80) REVERT: A 446 ARG cc_start: 0.7585 (tpt170) cc_final: 0.7203 (ttt180) REVERT: B 203 ARG cc_start: 0.6941 (mtp-110) cc_final: 0.6250 (mtm180) outliers start: 18 outliers final: 14 residues processed: 88 average time/residue: 0.0517 time to fit residues: 6.1527 Evaluate side-chains 91 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.086 ------------------------------------------------------------------------------- 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 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 189 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 378 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: 20.0000 chunk 50 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 30.0000 chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 0.0070 chunk 19 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.223633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.179287 restraints weight = 5799.478| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 3.77 r_work: 0.4088 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.5802 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= 0.123 Angle : 0.650 10.777 5584 Z= 0.323 Chirality : 0.042 0.129 661 Planarity : 0.004 0.062 715 Dihedral : 5.615 48.350 628 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 6.79 % Allowed : 31.48 % Favored : 61.73 % 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 aren not related in a simple way. whole: 0.77 (0.37), residues: 585 helix: 1.07 (0.30), residues: 339 sheet: 2.03 (0.51), residues: 109 loop : -2.25 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 261 TYR 0.013 0.001 TYR A 113 PHE 0.043 0.002 PHE A 332 TRP 0.022 0.001 TRP A 18 HIS 0.001 0.000 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 4091) covalent geometry : angle 0.64950 ( 5584) hydrogen bonds : bond 0.03802 ( 281) hydrogen bonds : angle 4.02196 ( 819) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1085.14 seconds wall clock time: 19 minutes 12.74 seconds (1152.74 seconds total)