Starting phenix.real_space_refine on Fri Dec 27 12:38:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hru_34980/12_2024/8hru_34980.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hru_34980/12_2024/8hru_34980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hru_34980/12_2024/8hru_34980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hru_34980/12_2024/8hru_34980.map" model { file = "/net/cci-nas-00/data/ceres_data/8hru_34980/12_2024/8hru_34980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hru_34980/12_2024/8hru_34980.cif" } resolution = 3.9 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= 0.007 sd= 0.066 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 29 5.16 5 C 3115 2.51 5 N 806 2.21 5 O 920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4870 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Time building chain proxies: 3.55, per 1000 atoms: 0.73 Number of scatterers: 4870 At special positions: 0 Unit cell: (85.324, 85.324, 71.96, 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 29 16.00 O 920 8.00 N 806 7.00 C 3115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.04 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: 1.20 Conformation dependent library (CDL) restraints added in 726.9 milliseconds 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 3 sheets defined 64.5% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 5.108A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.730A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.891A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.848A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.578A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.567A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 167 removed outlier: 3.585A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.752A pdb=" N GLU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 167 through 172' Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.563A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 220 through 249 removed outlier: 3.952A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.863A pdb=" N MET A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.606A pdb=" N LEU A 278 " --> pdb=" O TRP A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 removed outlier: 4.057A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.569A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.895A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.607A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.838A pdb=" N HIS A 401 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.709A pdb=" N ILE A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.643A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.260A pdb=" N MET A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.955A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.679A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.750A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 4.154A pdb=" N GLU A 564 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.793A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.631A pdb=" N ASP A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 removed outlier: 4.361A pdb=" N VAL A 132 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 142 " --> pdb=" O VAL A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.845A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.838A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 639 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: 1.58 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1578 1.35 - 1.47: 1270 1.47 - 1.59: 2107 1.59 - 1.71: 2 1.71 - 1.83: 50 Bond restraints: 5007 Sorted by residual: bond pdb=" CG PRO A 289 " pdb=" CD PRO A 289 " ideal model delta sigma weight residual 1.503 1.272 0.231 3.40e-02 8.65e+02 4.61e+01 bond pdb=" N PRO A 289 " pdb=" CD PRO A 289 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.93e+01 bond pdb=" CB PRO A 289 " pdb=" CG PRO A 289 " ideal model delta sigma weight residual 1.492 1.686 -0.194 5.00e-02 4.00e+02 1.51e+01 bond pdb=" CB PRO A 258 " pdb=" CG PRO A 258 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.69e+00 bond pdb=" N PRO A 289 " pdb=" CA PRO A 289 " ideal model delta sigma weight residual 1.469 1.444 0.024 1.28e-02 6.10e+03 3.62e+00 ... (remaining 5002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 6730 3.54 - 7.07: 57 7.07 - 10.61: 11 10.61 - 14.15: 3 14.15 - 17.69: 2 Bond angle restraints: 6803 Sorted by residual: angle pdb=" CA PRO A 289 " pdb=" N PRO A 289 " pdb=" CD PRO A 289 " ideal model delta sigma weight residual 112.00 94.31 17.69 1.40e+00 5.10e-01 1.60e+02 angle pdb=" N PRO A 289 " pdb=" CD PRO A 289 " pdb=" CG PRO A 289 " ideal model delta sigma weight residual 103.20 88.77 14.43 1.50e+00 4.44e-01 9.25e+01 angle pdb=" CA PRO A 289 " pdb=" CB PRO A 289 " pdb=" CG PRO A 289 " ideal model delta sigma weight residual 104.50 92.34 12.16 1.90e+00 2.77e-01 4.09e+01 angle pdb=" CA PRO A 258 " pdb=" N PRO A 258 " pdb=" CD PRO A 258 " ideal model delta sigma weight residual 112.00 105.47 6.53 1.40e+00 5.10e-01 2.18e+01 angle pdb=" CA LYS A 353 " pdb=" CB LYS A 353 " pdb=" CG LYS A 353 " ideal model delta sigma weight residual 114.10 121.64 -7.54 2.00e+00 2.50e-01 1.42e+01 ... (remaining 6798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 2461 16.24 - 32.48: 363 32.48 - 48.71: 101 48.71 - 64.95: 18 64.95 - 81.19: 16 Dihedral angle restraints: 2959 sinusoidal: 1205 harmonic: 1754 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 133.57 -40.57 1 1.00e+01 1.00e-02 2.31e+01 dihedral pdb=" CA CYS A 530 " pdb=" C CYS A 530 " pdb=" N GLN A 531 " pdb=" CA GLN A 531 " ideal model delta harmonic sigma weight residual 180.00 158.21 21.79 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA MET A 579 " pdb=" C MET A 579 " pdb=" N ASN A 580 " pdb=" CA ASN A 580 " ideal model delta harmonic sigma weight residual -180.00 -162.91 -17.09 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 2956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 538 0.053 - 0.106: 144 0.106 - 0.159: 23 0.159 - 0.212: 3 0.212 - 0.265: 2 Chirality restraints: 710 Sorted by residual: chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB THR A 118 " pdb=" CA THR A 118 " pdb=" OG1 THR A 118 " pdb=" CG2 THR A 118 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CG LEU A 391 " pdb=" CB LEU A 391 " pdb=" CD1 LEU A 391 " pdb=" CD2 LEU A 391 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.35e-01 ... (remaining 707 not shown) Planarity restraints: 881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 288 " -0.079 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO A 289 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 499 " 0.055 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO A 500 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 257 " -0.042 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO A 258 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.034 5.00e-02 4.00e+02 ... (remaining 878 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 62 2.58 - 3.16: 4222 3.16 - 3.74: 8348 3.74 - 4.32: 10856 4.32 - 4.90: 17365 Nonbonded interactions: 40853 Sorted by model distance: nonbonded pdb=" O ARG A 482 " pdb=" NH1 ARG A 482 " model vdw 2.000 3.120 nonbonded pdb=" O THR A 92 " pdb=" NE2 GLN A 96 " model vdw 2.165 3.120 nonbonded pdb=" O ALA A 403 " pdb=" NE2 GLN A 522 " model vdw 2.196 3.120 nonbonded pdb=" O THR A 118 " pdb=" OG1 THR A 122 " model vdw 2.204 3.040 nonbonded pdb=" NH2 ARG A 245 " pdb=" O PHE A 603 " model vdw 2.226 3.120 ... (remaining 40848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 0.190 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.990 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:3.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 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 : 0.006 0.231 5007 Z= 0.395 Angle : 0.980 17.687 6803 Z= 0.547 Chirality : 0.050 0.265 710 Planarity : 0.007 0.106 881 Dihedral : 17.398 81.191 1820 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.38 % Allowed : 26.57 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.35), residues: 595 helix: -0.65 (0.28), residues: 334 sheet: -2.31 (1.19), residues: 10 loop : -0.87 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 302 HIS 0.006 0.001 HIS A 265 PHE 0.024 0.002 PHE A 588 TYR 0.034 0.002 TYR A 521 ARG 0.011 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7125 (mmp) cc_final: 0.6647 (mmp) REVERT: A 350 ASP cc_start: 0.8261 (t0) cc_final: 0.6468 (t0) outliers start: 2 outliers final: 0 residues processed: 97 average time/residue: 0.1624 time to fit residues: 20.5749 Evaluate side-chains 87 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 34 optimal weight: 30.0000 chunk 53 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5007 Z= 0.234 Angle : 0.709 9.676 6803 Z= 0.352 Chirality : 0.045 0.160 710 Planarity : 0.005 0.070 881 Dihedral : 4.840 20.138 642 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.42 % Allowed : 21.82 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.94 (0.35), residues: 595 helix: -0.35 (0.28), residues: 347 sheet: -2.18 (1.40), residues: 10 loop : -0.76 (0.44), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 477 HIS 0.005 0.001 HIS A 265 PHE 0.017 0.002 PHE A 525 TYR 0.022 0.002 TYR A 521 ARG 0.007 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 LYS cc_start: 0.6017 (mttt) cc_final: 0.5392 (mttt) outliers start: 18 outliers final: 9 residues processed: 109 average time/residue: 0.1400 time to fit residues: 20.5240 Evaluate side-chains 91 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5007 Z= 0.182 Angle : 0.675 13.040 6803 Z= 0.328 Chirality : 0.044 0.160 710 Planarity : 0.004 0.047 881 Dihedral : 4.604 19.897 642 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.23 % Allowed : 22.77 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.36), residues: 595 helix: -0.08 (0.29), residues: 335 sheet: -2.13 (1.48), residues: 10 loop : -0.40 (0.45), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 594 HIS 0.003 0.001 HIS A 265 PHE 0.014 0.001 PHE A 512 TYR 0.038 0.002 TYR A 521 ARG 0.003 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TRP cc_start: 0.7635 (t-100) cc_final: 0.6051 (t-100) REVERT: A 237 TYR cc_start: 0.6882 (t80) cc_final: 0.6201 (t80) REVERT: A 297 MET cc_start: 0.8577 (mpp) cc_final: 0.8317 (mpp) REVERT: A 481 LYS cc_start: 0.5933 (mttt) cc_final: 0.5624 (mttt) REVERT: A 513 ILE cc_start: 0.6305 (OUTLIER) cc_final: 0.5890 (tp) outliers start: 17 outliers final: 9 residues processed: 112 average time/residue: 0.1591 time to fit residues: 23.6690 Evaluate side-chains 97 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5007 Z= 0.245 Angle : 0.712 12.755 6803 Z= 0.353 Chirality : 0.046 0.173 710 Planarity : 0.004 0.042 881 Dihedral : 4.834 19.035 642 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.36 % Allowed : 22.58 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.43 (0.36), residues: 595 helix: -0.01 (0.29), residues: 348 sheet: -2.18 (1.54), residues: 10 loop : -0.41 (0.45), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 594 HIS 0.004 0.001 HIS A 239 PHE 0.016 0.002 PHE A 512 TYR 0.024 0.002 TYR A 521 ARG 0.003 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8720 (m-30) cc_final: 0.8124 (p0) REVERT: A 168 TRP cc_start: 0.7974 (t-100) cc_final: 0.7106 (t-100) REVERT: A 237 TYR cc_start: 0.6964 (t80) cc_final: 0.6036 (t80) REVERT: A 525 PHE cc_start: 0.7632 (m-80) cc_final: 0.6898 (m-80) REVERT: A 541 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7841 (ptpt) REVERT: A 579 MET cc_start: 0.7029 (ppp) cc_final: 0.6812 (ppp) outliers start: 23 outliers final: 12 residues processed: 111 average time/residue: 0.1489 time to fit residues: 21.9631 Evaluate side-chains 100 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 30.0000 chunk 42 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 33 optimal weight: 8.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5007 Z= 0.183 Angle : 0.682 11.517 6803 Z= 0.328 Chirality : 0.044 0.173 710 Planarity : 0.004 0.041 881 Dihedral : 4.552 18.916 642 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.17 % Allowed : 22.77 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.20 (0.36), residues: 595 helix: 0.23 (0.29), residues: 338 sheet: -2.01 (1.56), residues: 10 loop : -0.39 (0.44), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 271 HIS 0.003 0.001 HIS A 239 PHE 0.010 0.001 PHE A 525 TYR 0.034 0.002 TYR A 521 ARG 0.003 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8704 (m-30) cc_final: 0.8134 (p0) REVERT: A 237 TYR cc_start: 0.7078 (t80) cc_final: 0.6654 (t80) REVERT: A 270 MET cc_start: 0.6514 (OUTLIER) cc_final: 0.6282 (tmm) REVERT: A 481 LYS cc_start: 0.6187 (mttt) cc_final: 0.5973 (mttt) REVERT: A 525 PHE cc_start: 0.7698 (m-10) cc_final: 0.6927 (m-80) REVERT: A 541 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7737 (ptpt) REVERT: A 557 MET cc_start: 0.7487 (tmm) cc_final: 0.7263 (tmm) REVERT: A 579 MET cc_start: 0.7222 (ppp) cc_final: 0.6956 (ppp) outliers start: 22 outliers final: 15 residues processed: 104 average time/residue: 0.1635 time to fit residues: 22.0819 Evaluate side-chains 103 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 32 optimal weight: 0.0270 chunk 41 optimal weight: 0.3980 overall best weight: 2.0844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5007 Z= 0.193 Angle : 0.706 10.983 6803 Z= 0.346 Chirality : 0.045 0.179 710 Planarity : 0.004 0.038 881 Dihedral : 4.495 18.557 642 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.42 % Allowed : 23.91 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.20 (0.36), residues: 595 helix: 0.10 (0.28), residues: 347 sheet: -1.86 (1.58), residues: 10 loop : -0.20 (0.45), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 271 HIS 0.002 0.001 HIS A 417 PHE 0.011 0.001 PHE A 390 TYR 0.029 0.002 TYR A 521 ARG 0.005 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8685 (m-30) cc_final: 0.8127 (p0) REVERT: A 123 MET cc_start: 0.8128 (mmp) cc_final: 0.7823 (mmt) REVERT: A 237 TYR cc_start: 0.7172 (t80) cc_final: 0.6695 (t80) REVERT: A 297 MET cc_start: 0.8465 (mpp) cc_final: 0.8241 (mpp) REVERT: A 481 LYS cc_start: 0.6137 (mttt) cc_final: 0.5899 (mttt) REVERT: A 525 PHE cc_start: 0.7684 (m-10) cc_final: 0.7007 (m-80) REVERT: A 541 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7716 (ptpt) REVERT: A 579 MET cc_start: 0.7131 (ppp) cc_final: 0.6873 (ppp) outliers start: 18 outliers final: 15 residues processed: 103 average time/residue: 0.1504 time to fit residues: 20.5526 Evaluate side-chains 100 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 5.9990 chunk 48 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5007 Z= 0.218 Angle : 0.731 10.687 6803 Z= 0.353 Chirality : 0.045 0.172 710 Planarity : 0.004 0.038 881 Dihedral : 4.520 18.060 642 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.80 % Allowed : 24.10 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.16 (0.37), residues: 595 helix: 0.15 (0.29), residues: 338 sheet: -1.84 (1.60), residues: 10 loop : -0.19 (0.45), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 168 HIS 0.002 0.001 HIS A 540 PHE 0.028 0.002 PHE A 588 TYR 0.027 0.002 TYR A 521 ARG 0.003 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9148 (mttt) cc_final: 0.8846 (mmtt) REVERT: A 67 ASP cc_start: 0.8678 (m-30) cc_final: 0.8112 (p0) REVERT: A 123 MET cc_start: 0.8237 (mmp) cc_final: 0.8018 (mmt) REVERT: A 168 TRP cc_start: 0.7995 (t-100) cc_final: 0.7728 (t-100) REVERT: A 228 HIS cc_start: 0.8806 (t70) cc_final: 0.7983 (t70) REVERT: A 237 TYR cc_start: 0.7302 (t80) cc_final: 0.6613 (t80) REVERT: A 541 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7729 (ptpt) REVERT: A 579 MET cc_start: 0.7101 (ppp) cc_final: 0.6803 (ppp) outliers start: 20 outliers final: 16 residues processed: 103 average time/residue: 0.1666 time to fit residues: 22.1090 Evaluate side-chains 101 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5007 Z= 0.217 Angle : 0.728 11.353 6803 Z= 0.353 Chirality : 0.045 0.220 710 Planarity : 0.004 0.051 881 Dihedral : 4.538 18.041 642 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.61 % Allowed : 24.86 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.21 (0.37), residues: 595 helix: 0.19 (0.29), residues: 332 sheet: -1.77 (1.42), residues: 12 loop : -0.32 (0.45), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 594 HIS 0.002 0.001 HIS A 540 PHE 0.024 0.002 PHE A 588 TYR 0.025 0.002 TYR A 521 ARG 0.008 0.001 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9153 (mttt) cc_final: 0.8836 (mmtt) REVERT: A 67 ASP cc_start: 0.8674 (m-30) cc_final: 0.8106 (p0) REVERT: A 168 TRP cc_start: 0.7722 (t-100) cc_final: 0.7463 (t-100) REVERT: A 228 HIS cc_start: 0.8813 (t70) cc_final: 0.7962 (t70) REVERT: A 237 TYR cc_start: 0.7407 (t80) cc_final: 0.6634 (t80) REVERT: A 541 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7754 (ptpt) REVERT: A 579 MET cc_start: 0.7070 (ppp) cc_final: 0.6790 (ppp) outliers start: 19 outliers final: 16 residues processed: 99 average time/residue: 0.1581 time to fit residues: 20.5272 Evaluate side-chains 100 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5007 Z= 0.183 Angle : 0.734 12.044 6803 Z= 0.352 Chirality : 0.044 0.198 710 Planarity : 0.004 0.036 881 Dihedral : 4.426 18.077 642 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.23 % Allowed : 26.57 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.15 (0.37), residues: 595 helix: 0.16 (0.29), residues: 337 sheet: -1.65 (1.42), residues: 12 loop : -0.19 (0.46), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 594 HIS 0.004 0.001 HIS A 417 PHE 0.022 0.001 PHE A 588 TYR 0.036 0.002 TYR A 521 ARG 0.006 0.001 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9140 (mttt) cc_final: 0.8874 (mmtt) REVERT: A 67 ASP cc_start: 0.8629 (m-30) cc_final: 0.8111 (p0) REVERT: A 168 TRP cc_start: 0.7619 (t-100) cc_final: 0.6952 (t-100) REVERT: A 174 LYS cc_start: 0.8953 (mptt) cc_final: 0.8413 (mmtp) REVERT: A 228 HIS cc_start: 0.8764 (t70) cc_final: 0.7880 (t70) REVERT: A 237 TYR cc_start: 0.7350 (t80) cc_final: 0.6643 (t80) REVERT: A 481 LYS cc_start: 0.6051 (pttt) cc_final: 0.4738 (ptpt) REVERT: A 525 PHE cc_start: 0.7510 (m-10) cc_final: 0.6790 (m-80) REVERT: A 541 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7669 (ptpt) REVERT: A 579 MET cc_start: 0.7039 (ppp) cc_final: 0.6770 (ppp) REVERT: A 595 LEU cc_start: 0.8312 (mm) cc_final: 0.7754 (mm) outliers start: 17 outliers final: 15 residues processed: 102 average time/residue: 0.1621 time to fit residues: 21.5140 Evaluate side-chains 103 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 37 optimal weight: 0.0970 chunk 49 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5007 Z= 0.206 Angle : 0.764 11.326 6803 Z= 0.369 Chirality : 0.045 0.181 710 Planarity : 0.004 0.039 881 Dihedral : 4.497 20.760 642 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.23 % Allowed : 26.57 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.36 (0.37), residues: 595 helix: 0.07 (0.29), residues: 342 sheet: -1.58 (1.43), residues: 12 loop : -0.42 (0.46), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 168 HIS 0.004 0.001 HIS A 417 PHE 0.021 0.002 PHE A 588 TYR 0.034 0.002 TYR A 521 ARG 0.007 0.001 ARG A 460 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9168 (mttt) cc_final: 0.8864 (mmtt) REVERT: A 62 MET cc_start: 0.8730 (ptm) cc_final: 0.8384 (ptt) REVERT: A 67 ASP cc_start: 0.8629 (m-30) cc_final: 0.8112 (p0) REVERT: A 174 LYS cc_start: 0.8943 (mptt) cc_final: 0.8429 (mmtp) REVERT: A 228 HIS cc_start: 0.8806 (t70) cc_final: 0.7940 (t70) REVERT: A 237 TYR cc_start: 0.7411 (t80) cc_final: 0.6637 (t80) REVERT: A 476 LYS cc_start: 0.8282 (mmpt) cc_final: 0.7587 (mmmt) REVERT: A 481 LYS cc_start: 0.6157 (pttt) cc_final: 0.4105 (pttp) REVERT: A 483 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8609 (tm-30) REVERT: A 541 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7748 (ptpt) REVERT: A 579 MET cc_start: 0.7017 (ppp) cc_final: 0.6747 (ppp) REVERT: A 595 LEU cc_start: 0.8329 (mm) cc_final: 0.7806 (mm) outliers start: 17 outliers final: 14 residues processed: 99 average time/residue: 0.1699 time to fit residues: 21.7232 Evaluate side-chains 101 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 541 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 31 optimal weight: 0.0470 chunk 40 optimal weight: 9.9990 overall best weight: 1.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** 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 = 0.4380 r_free = 0.4380 target = 0.133379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.115162 restraints weight = 16100.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.118312 restraints weight = 10527.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.120394 restraints weight = 7602.694| |-----------------------------------------------------------------------------| r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5007 Z= 0.189 Angle : 0.765 11.422 6803 Z= 0.369 Chirality : 0.045 0.184 710 Planarity : 0.004 0.036 881 Dihedral : 4.378 17.945 642 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.23 % Allowed : 27.32 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.34 (0.36), residues: 595 helix: 0.12 (0.29), residues: 338 sheet: -1.40 (1.43), residues: 12 loop : -0.47 (0.45), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 168 HIS 0.014 0.001 HIS A 417 PHE 0.019 0.001 PHE A 588 TYR 0.035 0.002 TYR A 521 ARG 0.005 0.001 ARG A 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1294.31 seconds wall clock time: 24 minutes 25.79 seconds (1465.79 seconds total)