Starting phenix.real_space_refine on Wed Mar 5 23:16:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lz0_30020/03_2025/6lz0_30020.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lz0_30020/03_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_30020/03_2025/6lz0_30020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lz0_30020/03_2025/6lz0_30020.map" model { file = "/net/cci-nas-00/data/ceres_data/6lz0_30020/03_2025/6lz0_30020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lz0_30020/03_2025/6lz0_30020.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 6, 'ASP:plan': 12, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 7} 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: 3.26, per 1000 atoms: 0.81 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: 1.21 Conformation dependent library (CDL) restraints added in 567.4 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: 0.50 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: 1.15 Time building geometry restraints manager: 1.41 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.130 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.270 ------------------------------------------------------------------------------- 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= 0.570 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 : 17.43 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.020 0.001 TRP A 424 HIS 0.004 0.001 HIS A 344 PHE 0.014 0.002 PHE A 332 TYR 0.016 0.001 TYR A 113 ARG 0.001 0.000 ARG A 328 *********************** 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 : 0.373 Fit side-chains REVERT: A 60 TRP cc_start: 0.6388 (OUTLIER) cc_final: 0.5669 (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: 0.1385 time to fit residues: 18.8595 Evaluate side-chains 78 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 48 optimal weight: 30.0000 chunk 43 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4700 r_free = 0.4700 target = 0.226930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.181450 restraints weight = 5625.873| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 3.60 r_work: 0.4121 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.2827 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= 0.227 Angle : 0.715 8.168 5584 Z= 0.372 Chirality : 0.044 0.146 661 Planarity : 0.005 0.064 715 Dihedral : 7.533 56.730 641 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.01 % Allowed : 20.06 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.34), residues: 585 helix: -0.62 (0.28), residues: 334 sheet: 1.00 (0.51), residues: 103 loop : -3.12 (0.46), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 424 HIS 0.004 0.001 HIS A 292 PHE 0.052 0.002 PHE A 332 TYR 0.023 0.002 TYR A 113 ARG 0.007 0.001 ARG B 203 *********************** 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 95 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.409 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 92 average time/residue: 0.1298 time to fit residues: 15.4935 Evaluate side-chains 80 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 54 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 44 optimal weight: 40.0000 chunk 52 optimal weight: 30.0000 chunk 22 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 50.0000 chunk 55 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 51 optimal weight: 30.0000 overall best weight: 2.2584 ------------------------------------------------------------------------------- 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 = 0.4536 r_free = 0.4536 target = 0.208270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.160770 restraints weight = 5662.896| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 3.28 r_work: 0.3895 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 4091 Z= 0.391 Angle : 0.831 8.086 5584 Z= 0.433 Chirality : 0.050 0.185 661 Planarity : 0.005 0.068 715 Dihedral : 6.378 57.654 628 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 9.26 % Allowed : 25.00 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.34), residues: 585 helix: -0.54 (0.27), residues: 341 sheet: 0.87 (0.51), residues: 110 loop : -2.87 (0.48), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 174 HIS 0.004 0.001 HIS B 205 PHE 0.052 0.003 PHE A 332 TYR 0.021 0.002 TYR A 138 ARG 0.003 0.001 ARG A 326 *********************** 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 124 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.414 Fit side-chains REVERT: A 149 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8018 (mp) REVERT: A 345 MET cc_start: 0.7069 (tmm) cc_final: 0.6403 (tmm) REVERT: A 376 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8725 (tm-30) REVERT: A 411 ARG cc_start: 0.6460 (ttt-90) cc_final: 0.4557 (ttp-170) REVERT: B 203 ARG cc_start: 0.6422 (mtp-110) cc_final: 0.6217 (mtm180) outliers start: 30 outliers final: 21 residues processed: 115 average time/residue: 0.1352 time to fit residues: 19.8725 Evaluate side-chains 104 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 100 LEU 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 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 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 A residue 435 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 57 optimal weight: 0.8980 chunk 42 optimal weight: 40.0000 chunk 40 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 37 optimal weight: 30.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.215104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.169204 restraints weight = 5557.049| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 3.20 r_work: 0.3910 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4091 Z= 0.338 Angle : 0.766 6.950 5584 Z= 0.395 Chirality : 0.047 0.184 661 Planarity : 0.005 0.068 715 Dihedral : 6.242 57.489 628 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 11.11 % Allowed : 27.78 % Favored : 61.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.35), residues: 585 helix: -0.15 (0.28), residues: 340 sheet: 0.94 (0.50), residues: 112 loop : -2.80 (0.51), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 174 HIS 0.012 0.002 HIS A 292 PHE 0.041 0.002 PHE A 332 TYR 0.026 0.002 TYR A 113 ARG 0.003 0.000 ARG A 196 *********************** 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 120 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 0.377 Fit side-chains REVERT: A 149 LEU cc_start: 0.8308 (mm) cc_final: 0.7952 (mp) REVERT: A 274 PHE cc_start: 0.8552 (m-80) cc_final: 0.8178 (m-10) REVERT: A 307 PHE cc_start: 0.7552 (t80) cc_final: 0.7243 (t80) REVERT: A 345 MET cc_start: 0.7056 (tmm) cc_final: 0.6531 (tmm) REVERT: A 378 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8184 (tt) REVERT: B 203 ARG cc_start: 0.6533 (mtp-110) cc_final: 0.6326 (mtm180) outliers start: 36 outliers final: 27 residues processed: 107 average time/residue: 0.1230 time to fit residues: 17.2594 Evaluate side-chains 108 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 88 VAL 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 132 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 286 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 30.0000 chunk 11 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 chunk 22 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 50 optimal weight: 0.0870 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.222728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.177374 restraints weight = 5623.821| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 3.39 r_work: 0.3987 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.5154 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= 0.189 Angle : 0.665 7.084 5584 Z= 0.337 Chirality : 0.042 0.148 661 Planarity : 0.004 0.065 715 Dihedral : 5.978 56.741 628 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 9.57 % Allowed : 29.32 % Favored : 61.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.36), residues: 585 helix: 0.43 (0.29), residues: 340 sheet: 1.00 (0.49), residues: 113 loop : -2.59 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 18 HIS 0.001 0.000 HIS B 205 PHE 0.039 0.002 PHE A 332 TYR 0.019 0.001 TYR A 113 ARG 0.001 0.000 ARG B 203 *********************** 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 117 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.389 Fit side-chains REVERT: A 149 LEU cc_start: 0.8182 (mm) cc_final: 0.7802 (mp) REVERT: A 274 PHE cc_start: 0.8543 (m-80) cc_final: 0.8183 (m-10) REVERT: A 307 PHE cc_start: 0.7342 (t80) cc_final: 0.7118 (t80) REVERT: A 345 MET cc_start: 0.6770 (tmm) cc_final: 0.6293 (tmm) REVERT: A 378 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8057 (tt) REVERT: A 387 PHE cc_start: 0.8400 (t80) cc_final: 0.7780 (t80) REVERT: B 203 ARG cc_start: 0.6493 (mtp-110) cc_final: 0.6216 (mtm180) outliers start: 31 outliers final: 23 residues processed: 106 average time/residue: 0.1284 time to fit residues: 17.5927 Evaluate side-chains 105 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 189 CYS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 281 LEU 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 386 ARG Chi-restraints excluded: chain A residue 391 VAL 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 435 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 216 VAL 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 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 54 optimal weight: 50.0000 chunk 47 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.222261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.179976 restraints weight = 5769.714| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 3.57 r_work: 0.4183 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.5393 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= 0.176 Angle : 0.647 7.483 5584 Z= 0.328 Chirality : 0.042 0.149 661 Planarity : 0.004 0.064 715 Dihedral : 5.830 56.177 628 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 8.33 % Allowed : 31.17 % Favored : 60.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.36), residues: 585 helix: 0.74 (0.30), residues: 333 sheet: 1.23 (0.50), residues: 111 loop : -2.48 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 18 HIS 0.002 0.001 HIS A 292 PHE 0.041 0.002 PHE A 332 TYR 0.017 0.001 TYR A 113 ARG 0.002 0.000 ARG A 196 *********************** 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 111 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.393 Fit side-chains REVERT: A 149 LEU cc_start: 0.8257 (mm) cc_final: 0.7842 (mp) REVERT: A 151 MET cc_start: 0.7808 (mmm) cc_final: 0.7473 (mmm) REVERT: A 345 MET cc_start: 0.6826 (tmm) cc_final: 0.6373 (tmm) REVERT: A 378 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8231 (tt) REVERT: B 203 ARG cc_start: 0.6580 (mtp-110) cc_final: 0.6367 (mtm180) outliers start: 27 outliers final: 19 residues processed: 100 average time/residue: 0.1292 time to fit residues: 17.0669 Evaluate side-chains 102 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 109 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 270 ASN 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 391 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 216 VAL 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 30 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 0.0870 chunk 16 optimal weight: 0.7980 chunk 52 optimal weight: 40.0000 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.222792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.179333 restraints weight = 5849.796| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 3.61 r_work: 0.4148 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.5591 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= 0.185 Angle : 0.660 12.694 5584 Z= 0.328 Chirality : 0.042 0.137 661 Planarity : 0.004 0.063 715 Dihedral : 5.799 57.335 628 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 8.95 % Allowed : 31.79 % Favored : 59.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.36), residues: 585 helix: 0.84 (0.30), residues: 333 sheet: 1.49 (0.52), residues: 109 loop : -2.42 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 18 HIS 0.001 0.000 HIS B 205 PHE 0.042 0.002 PHE A 332 TYR 0.015 0.001 TYR A 113 ARG 0.001 0.000 ARG A 196 *********************** 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 109 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.424 Fit side-chains REVERT: A 69 MET cc_start: 0.7984 (ttt) cc_final: 0.7680 (ttm) REVERT: A 149 LEU cc_start: 0.8291 (mm) cc_final: 0.7874 (mp) REVERT: A 151 MET cc_start: 0.7772 (mmm) cc_final: 0.7477 (mmm) REVERT: A 345 MET cc_start: 0.6695 (tmm) cc_final: 0.6254 (tmm) REVERT: A 378 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8252 (tt) REVERT: A 419 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.7117 (t80) outliers start: 29 outliers final: 24 residues processed: 99 average time/residue: 0.1439 time to fit residues: 18.8486 Evaluate side-chains 105 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 TYR 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 265 LEU Chi-restraints excluded: chain A residue 270 ASN 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 386 ARG Chi-restraints excluded: chain A residue 391 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 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 216 VAL 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: 1.9990 chunk 48 optimal weight: 50.0000 chunk 3 optimal weight: 0.6980 chunk 50 optimal weight: 0.0970 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 41 optimal weight: 30.0000 chunk 43 optimal weight: 50.0000 chunk 27 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.223961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.183397 restraints weight = 5664.103| |-----------------------------------------------------------------------------| r_work (start): 0.4318 rms_B_bonded: 3.48 r_work: 0.4217 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.5713 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= 0.182 Angle : 0.650 12.265 5584 Z= 0.325 Chirality : 0.042 0.135 661 Planarity : 0.004 0.061 715 Dihedral : 5.665 52.466 628 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 8.64 % Allowed : 32.41 % Favored : 58.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.37), residues: 585 helix: 0.96 (0.29), residues: 339 sheet: 1.70 (0.53), residues: 109 loop : -2.44 (0.50), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 18 HIS 0.001 0.000 HIS A 292 PHE 0.044 0.002 PHE A 332 TYR 0.014 0.001 TYR A 113 ARG 0.002 0.000 ARG B 203 *********************** 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 105 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.393 Fit side-chains REVERT: A 149 LEU cc_start: 0.8264 (mm) cc_final: 0.7855 (mp) REVERT: A 151 MET cc_start: 0.7756 (mmm) cc_final: 0.7481 (mmm) REVERT: A 294 SER cc_start: 0.8268 (OUTLIER) cc_final: 0.7664 (p) REVERT: A 345 MET cc_start: 0.6562 (tmm) cc_final: 0.6148 (tmm) REVERT: A 378 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8224 (tt) REVERT: A 419 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.7031 (t80) outliers start: 28 outliers final: 23 residues processed: 96 average time/residue: 0.1285 time to fit residues: 15.9994 Evaluate side-chains 102 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 62 SER 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 294 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 346 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 391 VAL 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 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 216 VAL 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 4 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 330 GLN B 115 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.221229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.179903 restraints weight = 5826.174| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 3.55 r_work: 0.4179 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.5790 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= 0.198 Angle : 0.648 12.314 5584 Z= 0.325 Chirality : 0.042 0.135 661 Planarity : 0.004 0.060 715 Dihedral : 5.589 50.252 628 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 10.19 % Allowed : 30.86 % Favored : 58.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.37), residues: 585 helix: 0.97 (0.29), residues: 340 sheet: 1.93 (0.53), residues: 107 loop : -2.43 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 18 HIS 0.001 0.000 HIS B 205 PHE 0.044 0.002 PHE A 332 TYR 0.014 0.001 TYR A 113 ARG 0.004 0.000 ARG B 203 *********************** 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 110 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.421 Fit side-chains REVERT: A 149 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7873 (mp) REVERT: A 151 MET cc_start: 0.7768 (mmm) cc_final: 0.7434 (mmm) REVERT: A 294 SER cc_start: 0.8251 (OUTLIER) cc_final: 0.7627 (p) REVERT: A 345 MET cc_start: 0.6565 (tmm) cc_final: 0.6130 (tmm) REVERT: A 378 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8240 (tt) REVERT: A 419 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7076 (t80) outliers start: 33 outliers final: 26 residues processed: 98 average time/residue: 0.1382 time to fit residues: 17.5742 Evaluate side-chains 107 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 77 SER 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 270 ASN Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 294 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 346 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 391 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 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 216 VAL 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 44 optimal weight: 50.0000 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 41 optimal weight: 40.0000 chunk 26 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.221258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.180153 restraints weight = 5754.098| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 3.50 r_work: 0.4183 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.5854 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= 0.199 Angle : 0.655 12.204 5584 Z= 0.329 Chirality : 0.042 0.133 661 Planarity : 0.004 0.061 715 Dihedral : 5.620 49.465 628 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 10.19 % Allowed : 30.86 % Favored : 58.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.37), residues: 585 helix: 1.01 (0.29), residues: 339 sheet: 1.97 (0.53), residues: 107 loop : -2.34 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 18 HIS 0.001 0.000 HIS B 205 PHE 0.045 0.002 PHE A 332 TYR 0.014 0.001 TYR A 113 ARG 0.004 0.000 ARG B 203 ********************** 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 108 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 0.397 Fit side-chains REVERT: A 149 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7863 (mp) REVERT: A 151 MET cc_start: 0.7776 (mmm) cc_final: 0.7426 (mmm) REVERT: A 294 SER cc_start: 0.8214 (OUTLIER) cc_final: 0.7603 (p) REVERT: A 345 MET cc_start: 0.6559 (tmm) cc_final: 0.6118 (tmm) REVERT: A 378 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8268 (tt) REVERT: A 419 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7136 (t80) outliers start: 33 outliers final: 28 residues processed: 97 average time/residue: 0.1287 time to fit residues: 16.2656 Evaluate side-chains 104 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 132 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 270 ASN Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 294 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 346 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 391 VAL 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 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 216 VAL 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 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.0010 chunk 53 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 44 optimal weight: 50.0000 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 6 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.224052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.182383 restraints weight = 5725.734| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 3.58 r_work: 0.4267 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.5976 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= 0.174 Angle : 0.655 12.347 5584 Z= 0.325 Chirality : 0.041 0.116 661 Planarity : 0.004 0.060 715 Dihedral : 5.720 56.185 628 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 9.26 % Allowed : 31.79 % Favored : 58.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.37), residues: 585 helix: 1.15 (0.30), residues: 339 sheet: 2.02 (0.52), residues: 107 loop : -2.34 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 18 HIS 0.001 0.000 HIS B 115 PHE 0.044 0.002 PHE A 332 TYR 0.014 0.001 TYR A 113 ARG 0.002 0.000 ARG A 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2325.73 seconds wall clock time: 40 minutes 51.95 seconds (2451.95 seconds total)