Starting phenix.real_space_refine on Mon Dec 30 04:07:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b8g_15913/12_2024/8b8g_15913.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b8g_15913/12_2024/8b8g_15913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b8g_15913/12_2024/8b8g_15913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b8g_15913/12_2024/8b8g_15913.map" model { file = "/net/cci-nas-00/data/ceres_data/8b8g_15913/12_2024/8b8g_15913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b8g_15913/12_2024/8b8g_15913.cif" } resolution = 3.39 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= 0.001 sd= 0.017 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 80 5.16 5 C 7946 2.51 5 N 1944 2.21 5 O 2116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12086 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 6043 Classifications: {'peptide': 732} Link IDs: {'PTRANS': 34, 'TRANS': 697} Chain breaks: 6 Restraints were copied for chains: B Time building chain proxies: 12.35, per 1000 atoms: 1.02 Number of scatterers: 12086 At special positions: 0 Unit cell: (119.784, 89.838, 119.784, 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 80 16.00 O 2116 8.00 N 1944 7.00 C 7946 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.02 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: 3.29 Conformation dependent library (CDL) restraints added in 1.9 seconds 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2788 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 64.1% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 91 through 109 Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.742A pdb=" N PHE A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 294 through 327 Processing helix chain 'A' and resid 331 through 338 removed outlier: 3.919A pdb=" N LYS A 335 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N CYS A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.541A pdb=" N GLN A 345 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 346' Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.732A pdb=" N ILE A 363 " --> pdb=" O ARG A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 376 through 409 removed outlier: 3.561A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 Processing helix chain 'A' and resid 448 through 489 removed outlier: 3.748A pdb=" N THR A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 539 removed outlier: 3.970A pdb=" N LYS A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 572 removed outlier: 4.107A pdb=" N ILE A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 636 Proline residue: A 628 - end of helix removed outlier: 3.595A pdb=" N GLY A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 removed outlier: 3.502A pdb=" N HIS A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 681 removed outlier: 3.877A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 685 Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.524A pdb=" N LEU A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 747 removed outlier: 3.916A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 759 Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.828A pdb=" N LEU A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'A' and resid 861 through 877 Processing helix chain 'B' and resid 91 through 109 Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.742A pdb=" N PHE B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 233 through 240 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 284 through 291 Processing helix chain 'B' and resid 294 through 327 Processing helix chain 'B' and resid 331 through 338 removed outlier: 3.919A pdb=" N LYS B 335 " --> pdb=" O CYS B 331 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N CYS B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 346 removed outlier: 3.541A pdb=" N GLN B 345 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 346 " --> pdb=" O GLY B 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 342 through 346' Processing helix chain 'B' and resid 360 through 363 removed outlier: 3.732A pdb=" N ILE B 363 " --> pdb=" O ARG B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 364 through 372 Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.561A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 427 Processing helix chain 'B' and resid 448 through 489 removed outlier: 3.748A pdb=" N THR B 487 " --> pdb=" O ILE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 539 removed outlier: 3.970A pdb=" N LYS B 530 " --> pdb=" O THR B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 572 removed outlier: 4.106A pdb=" N ILE B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 636 Proline residue: B 628 - end of helix removed outlier: 3.595A pdb=" N GLY B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG B 636 " --> pdb=" O ASN B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 655 removed outlier: 3.503A pdb=" N HIS B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 681 removed outlier: 3.877A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 685 Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.524A pdb=" N LEU B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 3.916A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 759 Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.828A pdb=" N LEU B 781 " --> pdb=" O ILE B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 877 Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 116 Processing sheet with id=AA2, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AA3, first strand: chain 'B' and resid 111 through 116 Processing sheet with id=AA4, first strand: chain 'B' and resid 784 through 785 720 hydrogen bonds defined for protein. 2130 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: 3.37 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3688 1.34 - 1.46: 2730 1.46 - 1.57: 5884 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 12422 Sorted by residual: bond pdb=" N TYR B 564 " pdb=" CA TYR B 564 " ideal model delta sigma weight residual 1.457 1.443 0.014 1.33e-02 5.65e+03 1.14e+00 bond pdb=" N TYR A 564 " pdb=" CA TYR A 564 " ideal model delta sigma weight residual 1.457 1.443 0.014 1.33e-02 5.65e+03 1.06e+00 bond pdb=" C ASN B 562 " pdb=" O ASN B 562 " ideal model delta sigma weight residual 1.235 1.247 -0.012 1.26e-02 6.30e+03 8.85e-01 bond pdb=" C ASN A 562 " pdb=" O ASN A 562 " ideal model delta sigma weight residual 1.235 1.247 -0.012 1.26e-02 6.30e+03 8.62e-01 bond pdb=" CA ASN A 796 " pdb=" C ASN A 796 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.26e-02 6.30e+03 8.30e-01 ... (remaining 12417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 16671 2.14 - 4.27: 169 4.27 - 6.41: 10 6.41 - 8.55: 0 8.55 - 10.68: 2 Bond angle restraints: 16852 Sorted by residual: angle pdb=" C ALA A 245 " pdb=" N PHE A 246 " pdb=" CA PHE A 246 " ideal model delta sigma weight residual 123.15 112.47 10.68 2.23e+00 2.01e-01 2.29e+01 angle pdb=" C ALA B 245 " pdb=" N PHE B 246 " pdb=" CA PHE B 246 " ideal model delta sigma weight residual 123.15 112.49 10.66 2.23e+00 2.01e-01 2.29e+01 angle pdb=" N ILE B 233 " pdb=" CA ILE B 233 " pdb=" C ILE B 233 " ideal model delta sigma weight residual 111.90 108.85 3.05 8.10e-01 1.52e+00 1.42e+01 angle pdb=" N ILE A 233 " pdb=" CA ILE A 233 " pdb=" C ILE A 233 " ideal model delta sigma weight residual 111.90 108.86 3.04 8.10e-01 1.52e+00 1.41e+01 angle pdb=" N ILE A 279 " pdb=" CA ILE A 279 " pdb=" C ILE A 279 " ideal model delta sigma weight residual 112.96 109.40 3.56 1.00e+00 1.00e+00 1.27e+01 ... (remaining 16847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 6715 17.67 - 35.33: 418 35.33 - 53.00: 130 53.00 - 70.67: 34 70.67 - 88.34: 10 Dihedral angle restraints: 7307 sinusoidal: 2973 harmonic: 4334 Sorted by residual: dihedral pdb=" CB CYS A 338 " pdb=" SG CYS A 338 " pdb=" SG CYS A 365 " pdb=" CB CYS A 365 " ideal model delta sinusoidal sigma weight residual 93.00 58.46 34.54 1 1.00e+01 1.00e-02 1.69e+01 dihedral pdb=" CA TYR A 222 " pdb=" C TYR A 222 " pdb=" N GLN A 223 " pdb=" CA GLN A 223 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA TYR B 222 " pdb=" C TYR B 222 " pdb=" N GLN B 223 " pdb=" CA GLN B 223 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 7304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1130 0.032 - 0.063: 512 0.063 - 0.095: 141 0.095 - 0.127: 51 0.127 - 0.158: 2 Chirality restraints: 1836 Sorted by residual: chirality pdb=" CA ILE A 762 " pdb=" N ILE A 762 " pdb=" C ILE A 762 " pdb=" CB ILE A 762 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA ILE B 762 " pdb=" N ILE B 762 " pdb=" C ILE B 762 " pdb=" CB ILE B 762 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA PRO A 686 " pdb=" N PRO A 686 " pdb=" C PRO A 686 " pdb=" CB PRO A 686 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 1833 not shown) Planarity restraints: 2098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 763 " 0.043 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO A 764 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 764 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 764 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 763 " -0.043 5.00e-02 4.00e+02 6.40e-02 6.54e+00 pdb=" N PRO B 764 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 762 " 0.035 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO B 763 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 763 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 763 " 0.029 5.00e-02 4.00e+02 ... (remaining 2095 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 141 2.60 - 3.18: 11231 3.18 - 3.75: 19920 3.75 - 4.33: 24887 4.33 - 4.90: 41161 Nonbonded interactions: 97340 Sorted by model distance: nonbonded pdb=" SG CYS B 338 " pdb=" SG CYS B 365 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS B 352 " pdb=" SG CYS B 356 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS B 349 " pdb=" SG CYS B 807 " model vdw 2.030 3.760 nonbonded pdb=" OG1 THR A 307 " pdb=" OD1 ASN A 696 " model vdw 2.096 3.040 nonbonded pdb=" OG1 THR B 307 " pdb=" OD1 ASN B 696 " model vdw 2.097 3.040 ... (remaining 97335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.950 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 33.730 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 0.004 0.032 12422 Z= 0.271 Angle : 0.556 10.682 16852 Z= 0.310 Chirality : 0.040 0.158 1836 Planarity : 0.005 0.064 2098 Dihedral : 13.754 88.336 4510 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 7.59 % Allowed : 11.53 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.87 (0.23), residues: 1436 helix: 1.72 (0.17), residues: 880 sheet: -2.17 (0.52), residues: 76 loop : -1.10 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 397 HIS 0.002 0.001 HIS B 249 PHE 0.014 0.001 PHE B 560 TYR 0.015 0.001 TYR B 306 ARG 0.002 0.000 ARG B 808 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 183 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7170 (pm20) REVERT: A 243 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.8724 (tppp) REVERT: A 385 PHE cc_start: 0.9255 (t80) cc_final: 0.8999 (t80) REVERT: A 404 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8365 (mm) REVERT: A 405 GLU cc_start: 0.9410 (tm-30) cc_final: 0.9175 (tm-30) REVERT: A 417 GLU cc_start: 0.8950 (tp30) cc_final: 0.8592 (tp30) REVERT: A 533 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8756 (mp) REVERT: A 534 MET cc_start: 0.8164 (mpt) cc_final: 0.7723 (mpt) REVERT: A 557 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8351 (mm) REVERT: A 657 GLN cc_start: 0.8902 (mp-120) cc_final: 0.8627 (mp10) REVERT: A 661 LYS cc_start: 0.8722 (mtpp) cc_final: 0.8476 (mtpp) REVERT: A 717 GLU cc_start: 0.8440 (mp0) cc_final: 0.8229 (mp0) REVERT: A 721 ASP cc_start: 0.8589 (p0) cc_final: 0.8340 (p0) REVERT: B 125 PHE cc_start: 0.8767 (m-80) cc_final: 0.8398 (m-10) REVERT: B 145 LYS cc_start: 0.4150 (OUTLIER) cc_final: 0.3887 (tppt) REVERT: B 233 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8493 (tp) REVERT: B 371 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8917 (tt) REVERT: B 417 GLU cc_start: 0.8977 (tp30) cc_final: 0.8527 (tp30) REVERT: B 462 PHE cc_start: 0.8700 (t80) cc_final: 0.8447 (t80) REVERT: B 555 MET cc_start: 0.9006 (mmm) cc_final: 0.8716 (mmt) REVERT: B 557 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8386 (mt) REVERT: B 671 MET cc_start: 0.9422 (OUTLIER) cc_final: 0.8677 (mpm) REVERT: B 721 ASP cc_start: 0.8552 (p0) cc_final: 0.8274 (p0) outliers start: 100 outliers final: 28 residues processed: 269 average time/residue: 0.2396 time to fit residues: 93.6994 Evaluate side-chains 161 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 823 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN A 720 GLN B 621 ASN B 696 ASN B 710 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12422 Z= 0.256 Angle : 0.600 10.923 16852 Z= 0.315 Chirality : 0.041 0.178 1836 Planarity : 0.005 0.067 2098 Dihedral : 8.572 87.275 1699 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.86 % Allowed : 16.01 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.08 (0.22), residues: 1436 helix: 1.80 (0.17), residues: 898 sheet: -2.20 (0.53), residues: 76 loop : -0.93 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 397 HIS 0.003 0.001 HIS A 768 PHE 0.019 0.002 PHE B 852 TYR 0.015 0.002 TYR B 569 ARG 0.002 0.000 ARG B 266 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 142 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.7876 (mpt180) cc_final: 0.7412 (mpt180) REVERT: A 78 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.6905 (pm20) REVERT: A 243 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.8608 (tppp) REVERT: A 385 PHE cc_start: 0.9260 (t80) cc_final: 0.9031 (t80) REVERT: A 404 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8257 (mm) REVERT: A 409 ASP cc_start: 0.9068 (OUTLIER) cc_final: 0.8210 (t0) REVERT: A 417 GLU cc_start: 0.8909 (tp30) cc_final: 0.8434 (tp30) REVERT: A 533 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8908 (mp) REVERT: A 534 MET cc_start: 0.8123 (mpt) cc_final: 0.7594 (mpt) REVERT: A 557 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8234 (mt) REVERT: A 661 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8361 (mtpp) REVERT: A 721 ASP cc_start: 0.8257 (p0) cc_final: 0.7527 (t0) REVERT: A 773 MET cc_start: 0.9324 (mmm) cc_final: 0.9104 (mmm) REVERT: B 125 PHE cc_start: 0.8817 (m-80) cc_final: 0.8481 (m-10) REVERT: B 349 CYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8321 (t) REVERT: B 371 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8787 (tt) REVERT: B 417 GLU cc_start: 0.8928 (tp30) cc_final: 0.8468 (tp30) REVERT: B 462 PHE cc_start: 0.8672 (t80) cc_final: 0.8458 (t80) REVERT: B 489 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6717 (mt) REVERT: B 555 MET cc_start: 0.9058 (mmm) cc_final: 0.8783 (mmt) REVERT: B 557 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8356 (mt) REVERT: B 671 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.8388 (mpm) REVERT: B 721 ASP cc_start: 0.8257 (p0) cc_final: 0.7404 (t0) outliers start: 64 outliers final: 35 residues processed: 196 average time/residue: 0.2153 time to fit residues: 64.1489 Evaluate side-chains 160 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 114 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 90 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 45 optimal weight: 0.2980 chunk 106 optimal weight: 10.0000 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 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN B 254 ASN B 621 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12422 Z= 0.166 Angle : 0.536 9.289 16852 Z= 0.282 Chirality : 0.040 0.175 1836 Planarity : 0.005 0.069 2098 Dihedral : 7.811 88.737 1678 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.25 % Allowed : 17.22 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.15 (0.22), residues: 1436 helix: 1.92 (0.16), residues: 896 sheet: -2.18 (0.54), residues: 76 loop : -1.02 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 397 HIS 0.002 0.000 HIS B 768 PHE 0.020 0.001 PHE B 852 TYR 0.014 0.001 TYR A 569 ARG 0.002 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 149 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.7939 (mpt180) cc_final: 0.7400 (mpt180) REVERT: A 78 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.6976 (pm20) REVERT: A 243 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.8846 (tppp) REVERT: A 255 TYR cc_start: 0.6986 (m-80) cc_final: 0.6702 (m-80) REVERT: A 385 PHE cc_start: 0.9252 (t80) cc_final: 0.9023 (t80) REVERT: A 404 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8370 (mm) REVERT: A 409 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8163 (t0) REVERT: A 417 GLU cc_start: 0.8854 (tp30) cc_final: 0.8451 (tp30) REVERT: A 534 MET cc_start: 0.8098 (mpt) cc_final: 0.7559 (mpt) REVERT: A 557 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8187 (mm) REVERT: A 631 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8036 (mpt) REVERT: A 661 LYS cc_start: 0.8711 (mtpp) cc_final: 0.8394 (mtpp) REVERT: A 684 SER cc_start: 0.9458 (t) cc_final: 0.9126 (p) REVERT: A 721 ASP cc_start: 0.8225 (p0) cc_final: 0.7763 (t0) REVERT: A 773 MET cc_start: 0.9373 (mmm) cc_final: 0.9169 (tpp) REVERT: B 125 PHE cc_start: 0.8792 (m-80) cc_final: 0.8544 (m-10) REVERT: B 371 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8739 (tt) REVERT: B 489 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6358 (mt) REVERT: B 555 MET cc_start: 0.9072 (mmm) cc_final: 0.8786 (mmt) REVERT: B 557 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8354 (mt) REVERT: B 569 TYR cc_start: 0.8916 (t80) cc_final: 0.8387 (t80) REVERT: B 670 GLU cc_start: 0.8464 (tm-30) cc_final: 0.7539 (tm-30) REVERT: B 671 MET cc_start: 0.9383 (OUTLIER) cc_final: 0.8192 (mpm) REVERT: B 721 ASP cc_start: 0.8180 (p0) cc_final: 0.7506 (t0) REVERT: B 722 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8847 (pt) REVERT: B 842 MET cc_start: 0.8897 (ttp) cc_final: 0.8574 (ttp) outliers start: 56 outliers final: 29 residues processed: 195 average time/residue: 0.2149 time to fit residues: 63.6410 Evaluate side-chains 166 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 0.2980 chunk 99 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12422 Z= 0.174 Angle : 0.525 8.609 16852 Z= 0.279 Chirality : 0.040 0.172 1836 Planarity : 0.005 0.070 2098 Dihedral : 7.145 88.841 1663 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.70 % Allowed : 17.45 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.20 (0.22), residues: 1436 helix: 1.97 (0.17), residues: 894 sheet: -2.14 (0.54), residues: 76 loop : -1.03 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.002 0.001 HIS B 768 PHE 0.026 0.001 PHE A 556 TYR 0.029 0.001 TYR A 306 ARG 0.002 0.000 ARG B 649 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 141 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: A 243 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8971 (tppp) REVERT: A 255 TYR cc_start: 0.6950 (m-80) cc_final: 0.6624 (m-80) REVERT: A 404 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8423 (mm) REVERT: A 409 ASP cc_start: 0.9038 (OUTLIER) cc_final: 0.8169 (t0) REVERT: A 417 GLU cc_start: 0.8825 (tp30) cc_final: 0.8412 (tp30) REVERT: A 534 MET cc_start: 0.8118 (mpt) cc_final: 0.7595 (mpt) REVERT: A 557 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8137 (mm) REVERT: A 631 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8025 (mpt) REVERT: A 661 LYS cc_start: 0.8609 (mtpp) cc_final: 0.8252 (mtpp) REVERT: A 684 SER cc_start: 0.9478 (t) cc_final: 0.9172 (p) REVERT: A 721 ASP cc_start: 0.8113 (p0) cc_final: 0.7631 (t0) REVERT: A 843 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8239 (tt0) REVERT: B 125 PHE cc_start: 0.8830 (m-80) cc_final: 0.8548 (m-10) REVERT: B 352 CYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8792 (p) REVERT: B 371 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8736 (tt) REVERT: B 489 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6433 (mt) REVERT: B 555 MET cc_start: 0.9097 (mmm) cc_final: 0.8810 (mmt) REVERT: B 557 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8349 (mt) REVERT: B 569 TYR cc_start: 0.8946 (t80) cc_final: 0.8337 (t80) REVERT: B 670 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7651 (tm-30) REVERT: B 671 MET cc_start: 0.9359 (OUTLIER) cc_final: 0.8199 (mpm) REVERT: B 721 ASP cc_start: 0.8115 (p0) cc_final: 0.7496 (t0) outliers start: 62 outliers final: 33 residues processed: 188 average time/residue: 0.2131 time to fit residues: 60.9075 Evaluate side-chains 168 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 97 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 126 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12422 Z= 0.300 Angle : 0.587 8.891 16852 Z= 0.314 Chirality : 0.042 0.191 1836 Planarity : 0.005 0.068 2098 Dihedral : 7.175 89.176 1661 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.93 % Allowed : 19.73 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.09 (0.22), residues: 1436 helix: 1.86 (0.16), residues: 900 sheet: -2.22 (0.54), residues: 76 loop : -1.04 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 705 HIS 0.003 0.001 HIS A 249 PHE 0.027 0.002 PHE A 556 TYR 0.028 0.002 TYR A 306 ARG 0.003 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 124 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.6856 (pm20) REVERT: A 243 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8763 (tppp) REVERT: A 255 TYR cc_start: 0.6984 (m-80) cc_final: 0.6725 (m-80) REVERT: A 404 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8417 (mm) REVERT: A 409 ASP cc_start: 0.9062 (OUTLIER) cc_final: 0.8170 (t0) REVERT: A 417 GLU cc_start: 0.8831 (tp30) cc_final: 0.8414 (tp30) REVERT: A 534 MET cc_start: 0.8156 (mpt) cc_final: 0.7688 (mpt) REVERT: A 557 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8268 (mm) REVERT: A 661 LYS cc_start: 0.8676 (mtpp) cc_final: 0.8403 (mtpp) REVERT: A 684 SER cc_start: 0.9551 (t) cc_final: 0.9231 (p) REVERT: A 721 ASP cc_start: 0.8250 (p0) cc_final: 0.7613 (t0) REVERT: B 352 CYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8852 (p) REVERT: B 371 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8885 (tt) REVERT: B 489 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6522 (mt) REVERT: B 555 MET cc_start: 0.9130 (mmm) cc_final: 0.8863 (mmt) REVERT: B 557 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8434 (mm) REVERT: B 569 TYR cc_start: 0.9029 (t80) cc_final: 0.8542 (t80) REVERT: B 601 CYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8263 (m) REVERT: B 670 GLU cc_start: 0.8513 (tm-30) cc_final: 0.7552 (tm-30) REVERT: B 671 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.8056 (mpm) REVERT: B 721 ASP cc_start: 0.8197 (p0) cc_final: 0.7608 (t0) outliers start: 65 outliers final: 43 residues processed: 174 average time/residue: 0.2272 time to fit residues: 59.2822 Evaluate side-chains 169 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 115 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 823 LYS Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12422 Z= 0.208 Angle : 0.541 7.555 16852 Z= 0.289 Chirality : 0.041 0.194 1836 Planarity : 0.005 0.069 2098 Dihedral : 7.019 89.327 1660 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.78 % Allowed : 20.94 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.22), residues: 1436 helix: 1.93 (0.17), residues: 898 sheet: -2.22 (0.54), residues: 76 loop : -1.07 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 273 HIS 0.002 0.001 HIS B 768 PHE 0.026 0.002 PHE A 385 TYR 0.024 0.001 TYR A 306 ARG 0.002 0.000 ARG B 649 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 129 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.6968 (pm20) REVERT: A 243 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8810 (tppp) REVERT: A 255 TYR cc_start: 0.6997 (m-80) cc_final: 0.6741 (m-80) REVERT: A 288 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8365 (tp) REVERT: A 404 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8468 (mm) REVERT: A 409 ASP cc_start: 0.9043 (OUTLIER) cc_final: 0.8155 (t0) REVERT: A 417 GLU cc_start: 0.8830 (tp30) cc_final: 0.8404 (tp30) REVERT: A 534 MET cc_start: 0.8119 (mpt) cc_final: 0.7659 (mpt) REVERT: A 556 PHE cc_start: 0.9185 (t80) cc_final: 0.8924 (t80) REVERT: A 557 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8206 (mm) REVERT: A 661 LYS cc_start: 0.8686 (mtpp) cc_final: 0.8383 (mtpp) REVERT: A 684 SER cc_start: 0.9553 (t) cc_final: 0.9221 (p) REVERT: A 721 ASP cc_start: 0.8172 (p0) cc_final: 0.7683 (t0) REVERT: B 352 CYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8993 (p) REVERT: B 371 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8898 (tt) REVERT: B 489 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6529 (mt) REVERT: B 555 MET cc_start: 0.9080 (mmm) cc_final: 0.8802 (mmt) REVERT: B 557 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8335 (mm) REVERT: B 569 TYR cc_start: 0.9052 (t80) cc_final: 0.8531 (t80) REVERT: B 601 CYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8279 (m) REVERT: B 670 GLU cc_start: 0.8494 (tm-30) cc_final: 0.7549 (tm-30) REVERT: B 671 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.8028 (mpm) REVERT: B 721 ASP cc_start: 0.8104 (p0) cc_final: 0.7668 (t0) outliers start: 63 outliers final: 44 residues processed: 177 average time/residue: 0.2257 time to fit residues: 59.8926 Evaluate side-chains 176 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 120 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 823 LYS Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 118 optimal weight: 0.0050 chunk 78 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 chunk 64 optimal weight: 6.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12422 Z= 0.179 Angle : 0.526 6.848 16852 Z= 0.281 Chirality : 0.040 0.199 1836 Planarity : 0.005 0.069 2098 Dihedral : 6.953 89.570 1660 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.48 % Allowed : 21.24 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.20 (0.22), residues: 1436 helix: 1.99 (0.17), residues: 898 sheet: -2.17 (0.53), residues: 76 loop : -1.10 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 273 HIS 0.002 0.001 HIS B 768 PHE 0.028 0.001 PHE A 385 TYR 0.024 0.001 TYR A 306 ARG 0.002 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 132 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.6913 (pm20) REVERT: A 243 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8941 (tppp) REVERT: A 255 TYR cc_start: 0.7023 (m-80) cc_final: 0.6806 (m-80) REVERT: A 288 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8348 (tp) REVERT: A 404 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8429 (mm) REVERT: A 409 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8079 (t0) REVERT: A 417 GLU cc_start: 0.8837 (tp30) cc_final: 0.8414 (tp30) REVERT: A 534 MET cc_start: 0.8060 (mpt) cc_final: 0.7601 (mpt) REVERT: A 557 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8165 (mm) REVERT: A 661 LYS cc_start: 0.8692 (mtpp) cc_final: 0.8396 (mtpp) REVERT: A 684 SER cc_start: 0.9547 (t) cc_final: 0.9210 (p) REVERT: A 721 ASP cc_start: 0.8141 (p0) cc_final: 0.7729 (t0) REVERT: A 773 MET cc_start: 0.9210 (mmm) cc_final: 0.8839 (tpt) REVERT: B 352 CYS cc_start: 0.9236 (OUTLIER) cc_final: 0.9013 (p) REVERT: B 371 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8882 (tt) REVERT: B 489 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6400 (mt) REVERT: B 555 MET cc_start: 0.8997 (mmm) cc_final: 0.8683 (mmt) REVERT: B 557 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8315 (mm) REVERT: B 569 TYR cc_start: 0.9032 (t80) cc_final: 0.8452 (t80) REVERT: B 601 CYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8247 (m) REVERT: B 670 GLU cc_start: 0.8500 (tm-30) cc_final: 0.7545 (tm-30) REVERT: B 671 MET cc_start: 0.9328 (OUTLIER) cc_final: 0.7960 (mpm) REVERT: B 721 ASP cc_start: 0.8182 (p0) cc_final: 0.7789 (t0) outliers start: 59 outliers final: 43 residues processed: 176 average time/residue: 0.2236 time to fit residues: 59.2394 Evaluate side-chains 177 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 122 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 823 LYS Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 89 optimal weight: 0.3980 chunk 95 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12422 Z= 0.180 Angle : 0.532 7.262 16852 Z= 0.284 Chirality : 0.040 0.202 1836 Planarity : 0.005 0.069 2098 Dihedral : 6.926 89.652 1660 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.55 % Allowed : 21.70 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.21 (0.22), residues: 1436 helix: 2.03 (0.17), residues: 900 sheet: -2.14 (0.53), residues: 76 loop : -1.18 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 273 HIS 0.002 0.001 HIS A 768 PHE 0.028 0.001 PHE A 385 TYR 0.023 0.001 TYR A 306 ARG 0.002 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 132 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.6876 (pm20) REVERT: A 225 MET cc_start: 0.6085 (tpt) cc_final: 0.5212 (pmm) REVERT: A 243 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.9017 (tppp) REVERT: A 255 TYR cc_start: 0.7026 (m-80) cc_final: 0.6816 (m-80) REVERT: A 404 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8468 (mm) REVERT: A 409 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8020 (t0) REVERT: A 417 GLU cc_start: 0.8835 (tp30) cc_final: 0.8430 (tp30) REVERT: A 534 MET cc_start: 0.8040 (mpt) cc_final: 0.7613 (mpt) REVERT: A 661 LYS cc_start: 0.8648 (mtpp) cc_final: 0.8370 (mtpp) REVERT: A 684 SER cc_start: 0.9544 (t) cc_final: 0.9208 (p) REVERT: A 721 ASP cc_start: 0.8177 (p0) cc_final: 0.7746 (t0) REVERT: B 352 CYS cc_start: 0.9237 (OUTLIER) cc_final: 0.9016 (p) REVERT: B 371 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8886 (tt) REVERT: B 555 MET cc_start: 0.9030 (mmm) cc_final: 0.8723 (mmt) REVERT: B 557 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8276 (mm) REVERT: B 569 TYR cc_start: 0.9025 (t80) cc_final: 0.8430 (t80) REVERT: B 601 CYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8234 (m) REVERT: B 670 GLU cc_start: 0.8506 (tm-30) cc_final: 0.7549 (tm-30) REVERT: B 671 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.7955 (mpm) REVERT: B 721 ASP cc_start: 0.8172 (p0) cc_final: 0.7787 (t0) outliers start: 60 outliers final: 48 residues processed: 176 average time/residue: 0.2234 time to fit residues: 59.4004 Evaluate side-chains 183 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 126 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 823 LYS Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 118 optimal weight: 0.0170 chunk 124 optimal weight: 0.7980 chunk 130 optimal weight: 0.4980 chunk 86 optimal weight: 0.6980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12422 Z= 0.157 Angle : 0.532 7.729 16852 Z= 0.282 Chirality : 0.040 0.208 1836 Planarity : 0.005 0.069 2098 Dihedral : 6.817 89.864 1658 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.02 % Allowed : 22.53 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.22), residues: 1436 helix: 2.06 (0.17), residues: 898 sheet: -1.93 (0.54), residues: 66 loop : -1.18 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 273 HIS 0.002 0.000 HIS B 143 PHE 0.028 0.001 PHE A 385 TYR 0.023 0.001 TYR A 306 ARG 0.001 0.000 ARG B 649 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.6827 (pm20) REVERT: A 143 HIS cc_start: 0.8814 (m90) cc_final: 0.8604 (m90) REVERT: A 225 MET cc_start: 0.6423 (tpt) cc_final: 0.5604 (pmm) REVERT: A 243 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.9025 (tppp) REVERT: A 255 TYR cc_start: 0.7058 (m-80) cc_final: 0.6854 (m-80) REVERT: A 409 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8026 (t0) REVERT: A 414 GLN cc_start: 0.8479 (mp10) cc_final: 0.8206 (mm110) REVERT: A 417 GLU cc_start: 0.8900 (tp30) cc_final: 0.8473 (tp30) REVERT: A 534 MET cc_start: 0.8015 (mpt) cc_final: 0.7583 (mpt) REVERT: A 659 MET cc_start: 0.8261 (ttp) cc_final: 0.8057 (tmm) REVERT: A 661 LYS cc_start: 0.8593 (mtpp) cc_final: 0.8317 (mtpp) REVERT: A 684 SER cc_start: 0.9536 (t) cc_final: 0.9187 (p) REVERT: A 721 ASP cc_start: 0.8142 (p0) cc_final: 0.7753 (t0) REVERT: B 352 CYS cc_start: 0.9239 (OUTLIER) cc_final: 0.9029 (p) REVERT: B 371 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8861 (tt) REVERT: B 555 MET cc_start: 0.8966 (mmm) cc_final: 0.8652 (mmt) REVERT: B 557 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8240 (mm) REVERT: B 569 TYR cc_start: 0.9002 (t80) cc_final: 0.8378 (t80) REVERT: B 601 CYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8200 (m) REVERT: B 670 GLU cc_start: 0.8501 (tm-30) cc_final: 0.7581 (tm-30) REVERT: B 671 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.7999 (mpm) REVERT: B 721 ASP cc_start: 0.8127 (p0) cc_final: 0.7801 (t0) outliers start: 53 outliers final: 40 residues processed: 177 average time/residue: 0.2222 time to fit residues: 59.3939 Evaluate side-chains 179 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 131 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 823 LYS Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 0.1980 chunk 84 optimal weight: 0.4980 chunk 65 optimal weight: 0.0470 chunk 96 optimal weight: 0.0770 chunk 145 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 12 optimal weight: 0.0570 chunk 89 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.1754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12422 Z= 0.141 Angle : 0.531 8.174 16852 Z= 0.280 Chirality : 0.040 0.210 1836 Planarity : 0.005 0.070 2098 Dihedral : 6.678 89.701 1656 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.34 % Allowed : 23.60 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.31 (0.22), residues: 1436 helix: 2.19 (0.17), residues: 878 sheet: -1.73 (0.55), residues: 66 loop : -1.27 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 397 HIS 0.002 0.000 HIS B 143 PHE 0.027 0.001 PHE A 852 TYR 0.027 0.001 TYR A 306 ARG 0.005 0.000 ARG A 713 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.6820 (pm20) REVERT: A 198 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6723 (mp) REVERT: A 225 MET cc_start: 0.6068 (tpt) cc_final: 0.5557 (pmm) REVERT: A 255 TYR cc_start: 0.7112 (m-80) cc_final: 0.6894 (m-80) REVERT: A 409 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8011 (t0) REVERT: A 414 GLN cc_start: 0.8457 (mp10) cc_final: 0.8217 (mm110) REVERT: A 417 GLU cc_start: 0.8896 (tp30) cc_final: 0.8442 (tp30) REVERT: A 534 MET cc_start: 0.7910 (mpt) cc_final: 0.7515 (mpt) REVERT: A 557 LEU cc_start: 0.8248 (mm) cc_final: 0.7826 (mm) REVERT: A 661 LYS cc_start: 0.8567 (mtpp) cc_final: 0.8284 (mtpp) REVERT: A 684 SER cc_start: 0.9510 (t) cc_final: 0.9158 (p) REVERT: A 721 ASP cc_start: 0.8145 (p0) cc_final: 0.7746 (t0) REVERT: B 352 CYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8964 (p) REVERT: B 371 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8825 (tt) REVERT: B 386 MET cc_start: 0.8164 (mtp) cc_final: 0.7938 (ttp) REVERT: B 557 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8148 (mm) REVERT: B 566 SER cc_start: 0.8537 (t) cc_final: 0.7948 (p) REVERT: B 569 TYR cc_start: 0.8942 (t80) cc_final: 0.8288 (t80) REVERT: B 609 LEU cc_start: 0.9519 (tt) cc_final: 0.9189 (tt) REVERT: B 671 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.8990 (mmp) REVERT: B 721 ASP cc_start: 0.8054 (p0) cc_final: 0.7809 (t0) outliers start: 44 outliers final: 32 residues processed: 183 average time/residue: 0.2272 time to fit residues: 63.2922 Evaluate side-chains 171 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 823 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 chunk 116 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 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 = 0.3631 r_free = 0.3631 target = 0.102746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.077536 restraints weight = 29449.873| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.49 r_work: 0.3003 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12422 Z= 0.208 Angle : 0.556 8.300 16852 Z= 0.297 Chirality : 0.041 0.201 1836 Planarity : 0.005 0.084 2098 Dihedral : 6.523 98.793 1650 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.41 % Allowed : 23.60 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: 1.29 (0.22), residues: 1436 helix: 2.10 (0.17), residues: 894 sheet: -1.82 (0.54), residues: 66 loop : -1.21 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 273 HIS 0.002 0.001 HIS B 143 PHE 0.029 0.002 PHE A 852 TYR 0.029 0.001 TYR A 569 ARG 0.004 0.000 ARG A 808 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2436.51 seconds wall clock time: 45 minutes 35.17 seconds (2735.17 seconds total)