Starting phenix.real_space_refine on Sat Aug 23 12:51:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b8g_15913/08_2025/8b8g_15913.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b8g_15913/08_2025/8b8g_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 { model { file = "/net/cci-nas-00/data/ceres_data/8b8g_15913/08_2025/8b8g_15913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b8g_15913/08_2025/8b8g_15913.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b8g_15913/08_2025/8b8g_15913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b8g_15913/08_2025/8b8g_15913.map" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.87, per 1000 atoms: 0.49 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=6, 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 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 592.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.39 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: 2.06 Time building geometry restraints manager: 1.49 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: 6723 17.67 - 35.33: 419 35.33 - 53.00: 130 53.00 - 70.67: 34 70.67 - 88.34: 10 Dihedral angle restraints: 7316 sinusoidal: 2982 harmonic: 4334 Sorted by residual: dihedral pdb=" CB CYS B 338 " pdb=" SG CYS B 338 " pdb=" SG CYS B 365 " pdb=" CB CYS B 365 " ideal model delta sinusoidal sigma weight residual 93.00 58.42 34.58 1 1.00e+01 1.00e-02 1.70e+01 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 ... (remaining 7313 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: 2.10 - 2.66: 187 2.66 - 3.22: 12430 3.22 - 3.78: 19830 3.78 - 4.34: 24482 4.34 - 4.90: 40402 Nonbonded interactions: 97331 Sorted by model distance: 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 nonbonded pdb=" O ILE A 744 " pdb=" OG SER A 748 " model vdw 2.162 3.040 nonbonded pdb=" O ILE B 744 " pdb=" OG SER B 748 " model vdw 2.162 3.040 nonbonded pdb=" O ALA B 571 " pdb=" OG1 THR B 747 " model vdw 2.174 3.040 ... (remaining 97326 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: 0.03 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: 1.150 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.690 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.920 ------------------------------------------------------------------------------- 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 12428 Z= 0.202 Angle : 0.558 10.682 16864 Z= 0.311 Chirality : 0.040 0.158 1836 Planarity : 0.005 0.064 2098 Dihedral : 13.754 88.336 4510 Min Nonbonded Distance : 2.096 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (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 ARG 0.002 0.000 ARG B 808 TYR 0.015 0.001 TYR B 306 PHE 0.014 0.001 PHE B 560 TRP 0.014 0.001 TRP A 397 HIS 0.002 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00430 (12422) covalent geometry : angle 0.55565 (16852) SS BOND : bond 0.00445 ( 6) SS BOND : angle 1.84431 ( 12) hydrogen bonds : bond 0.12148 ( 720) hydrogen bonds : angle 5.23664 ( 2130) *********************** 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 : 0.533 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: 0.1092 time to fit residues: 43.4692 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 : 0.504 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0170 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 A 657 GLN A 720 GLN B 621 ASN B 696 ASN B 710 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.102628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.077480 restraints weight = 28790.256| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.44 r_work: 0.3012 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12428 Z= 0.136 Angle : 0.575 10.525 16864 Z= 0.300 Chirality : 0.040 0.180 1836 Planarity : 0.005 0.068 2098 Dihedral : 8.508 87.731 1699 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.32 % Allowed : 16.31 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.22), residues: 1436 helix: 1.91 (0.17), residues: 892 sheet: -2.18 (0.54), residues: 76 loop : -0.94 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 266 TYR 0.014 0.001 TYR B 569 PHE 0.019 0.001 PHE B 852 TRP 0.013 0.001 TRP A 397 HIS 0.002 0.000 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00288 (12422) covalent geometry : angle 0.57429 (16852) SS BOND : bond 0.00539 ( 6) SS BOND : angle 1.05913 ( 12) hydrogen bonds : bond 0.05132 ( 720) hydrogen bonds : angle 4.45632 ( 2130) *********************** 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 215 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 158 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.7978 (mpt180) cc_final: 0.7531 (mpt180) REVERT: A 78 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7120 (pm20) REVERT: A 243 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.8844 (tppp) REVERT: A 385 PHE cc_start: 0.9221 (t80) cc_final: 0.9002 (t80) REVERT: A 404 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8293 (mm) REVERT: A 409 ASP cc_start: 0.9138 (OUTLIER) cc_final: 0.8192 (t0) REVERT: A 417 GLU cc_start: 0.9002 (tp30) cc_final: 0.8414 (tp30) REVERT: A 516 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8254 (pp) REVERT: A 534 MET cc_start: 0.7835 (mpt) cc_final: 0.7311 (mpt) REVERT: A 556 PHE cc_start: 0.9223 (t80) cc_final: 0.8986 (t80) REVERT: A 557 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7948 (mt) REVERT: A 661 LYS cc_start: 0.8755 (mtpp) cc_final: 0.8368 (mtpp) REVERT: A 721 ASP cc_start: 0.8307 (p0) cc_final: 0.7437 (t0) REVERT: A 773 MET cc_start: 0.9340 (mmm) cc_final: 0.9080 (mmm) REVERT: B 125 PHE cc_start: 0.8750 (m-80) cc_final: 0.8362 (m-10) REVERT: B 145 LYS cc_start: 0.4265 (OUTLIER) cc_final: 0.3912 (tppt) REVERT: B 371 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8628 (tt) REVERT: B 385 PHE cc_start: 0.9193 (t80) cc_final: 0.8960 (t80) REVERT: B 417 GLU cc_start: 0.9010 (tp30) cc_final: 0.8431 (tp30) REVERT: B 489 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6747 (mt) REVERT: B 555 MET cc_start: 0.8993 (mmm) cc_final: 0.8707 (mmt) REVERT: B 557 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8101 (mt) REVERT: B 609 LEU cc_start: 0.9348 (tp) cc_final: 0.9122 (tt) REVERT: B 671 MET cc_start: 0.9410 (OUTLIER) cc_final: 0.8423 (mpm) REVERT: B 721 ASP cc_start: 0.8340 (p0) cc_final: 0.7372 (t0) outliers start: 57 outliers final: 23 residues processed: 206 average time/residue: 0.0940 time to fit residues: 29.9329 Evaluate side-chains 162 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 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 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 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 320 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 738 VAL Chi-restraints excluded: chain B residue 770 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 74 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.102519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.077050 restraints weight = 29319.402| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.57 r_work: 0.2987 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12428 Z= 0.139 Angle : 0.542 9.616 16864 Z= 0.286 Chirality : 0.040 0.172 1836 Planarity : 0.005 0.069 2098 Dihedral : 7.538 88.323 1666 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.40 % Allowed : 17.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.22), residues: 1436 helix: 1.93 (0.16), residues: 896 sheet: -2.25 (0.53), residues: 76 loop : -0.98 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 649 TYR 0.014 0.001 TYR A 569 PHE 0.019 0.001 PHE B 852 TRP 0.012 0.001 TRP A 397 HIS 0.002 0.001 HIS A 768 Details of bonding type rmsd covalent geometry : bond 0.00300 (12422) covalent geometry : angle 0.54183 (16852) SS BOND : bond 0.00163 ( 6) SS BOND : angle 0.97275 ( 12) hydrogen bonds : bond 0.04956 ( 720) hydrogen bonds : angle 4.36973 ( 2130) *********************** 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 198 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 140 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8039 (mpt180) cc_final: 0.7466 (mpt180) REVERT: A 78 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7121 (pm20) REVERT: A 243 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.8848 (tppp) REVERT: A 255 TYR cc_start: 0.7157 (m-80) cc_final: 0.6845 (m-80) REVERT: A 404 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8340 (mm) REVERT: A 409 ASP cc_start: 0.9148 (OUTLIER) cc_final: 0.8163 (t0) REVERT: A 417 GLU cc_start: 0.8951 (tp30) cc_final: 0.8446 (tp30) REVERT: A 534 MET cc_start: 0.7912 (mpt) cc_final: 0.7417 (mpt) REVERT: A 556 PHE cc_start: 0.9263 (t80) cc_final: 0.9057 (t80) REVERT: A 557 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8012 (mm) REVERT: A 661 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8438 (mtpp) REVERT: A 721 ASP cc_start: 0.8356 (p0) cc_final: 0.7660 (t0) REVERT: A 773 MET cc_start: 0.9422 (mmm) cc_final: 0.9207 (tpp) REVERT: B 125 PHE cc_start: 0.8688 (m-80) cc_final: 0.8379 (m-10) REVERT: B 145 LYS cc_start: 0.4230 (OUTLIER) cc_final: 0.3798 (tppt) REVERT: B 371 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8631 (tt) REVERT: B 489 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6486 (mt) REVERT: B 555 MET cc_start: 0.8995 (mmm) cc_final: 0.8715 (mmt) REVERT: B 557 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8192 (mt) REVERT: B 569 TYR cc_start: 0.8912 (t80) cc_final: 0.8483 (t80) REVERT: B 721 ASP cc_start: 0.8270 (p0) cc_final: 0.7348 (t0) REVERT: B 722 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8843 (pt) outliers start: 58 outliers final: 29 residues processed: 189 average time/residue: 0.0954 time to fit residues: 27.6988 Evaluate side-chains 165 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 280 TYR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 307 THR 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 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 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 371 LEU Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 698 LEU 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 848 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 42 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 75 optimal weight: 0.2980 chunk 126 optimal weight: 0.4980 chunk 128 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** B 108 HIS B 621 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.102452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.077275 restraints weight = 29496.287| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.53 r_work: 0.3007 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12428 Z= 0.125 Angle : 0.524 8.427 16864 Z= 0.276 Chirality : 0.040 0.170 1836 Planarity : 0.005 0.070 2098 Dihedral : 7.301 88.872 1663 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.32 % Allowed : 18.29 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.22), residues: 1436 helix: 2.01 (0.16), residues: 894 sheet: -2.29 (0.52), residues: 76 loop : -1.00 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 701 TYR 0.029 0.001 TYR A 306 PHE 0.025 0.001 PHE A 385 TRP 0.011 0.001 TRP B 397 HIS 0.002 0.001 HIS A 768 Details of bonding type rmsd covalent geometry : bond 0.00262 (12422) covalent geometry : angle 0.52373 (16852) SS BOND : bond 0.00122 ( 6) SS BOND : angle 0.79601 ( 12) hydrogen bonds : bond 0.04723 ( 720) hydrogen bonds : angle 4.28057 ( 2130) *********************** 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 198 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 141 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7087 (pm20) REVERT: A 243 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.8939 (tppp) REVERT: A 255 TYR cc_start: 0.7052 (m-80) cc_final: 0.6697 (m-80) REVERT: A 288 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8364 (tp) REVERT: A 409 ASP cc_start: 0.9150 (OUTLIER) cc_final: 0.8167 (t0) REVERT: A 417 GLU cc_start: 0.8944 (tp30) cc_final: 0.8400 (tp30) REVERT: A 534 MET cc_start: 0.7897 (mpt) cc_final: 0.7394 (mpt) REVERT: A 556 PHE cc_start: 0.9221 (t80) cc_final: 0.8966 (t80) REVERT: A 557 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7939 (mm) REVERT: A 661 LYS cc_start: 0.8877 (mtpp) cc_final: 0.8523 (mtpp) REVERT: A 684 SER cc_start: 0.9484 (t) cc_final: 0.9138 (p) REVERT: A 721 ASP cc_start: 0.8265 (p0) cc_final: 0.7608 (t0) REVERT: A 773 MET cc_start: 0.9416 (mmm) cc_final: 0.9156 (tpp) REVERT: A 842 MET cc_start: 0.9114 (ttp) cc_final: 0.8826 (ttp) REVERT: B 125 PHE cc_start: 0.8739 (m-80) cc_final: 0.8424 (m-10) REVERT: B 145 LYS cc_start: 0.4460 (OUTLIER) cc_final: 0.4026 (tppt) REVERT: B 385 PHE cc_start: 0.9218 (t80) cc_final: 0.8991 (t80) REVERT: B 489 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6528 (mt) REVERT: B 555 MET cc_start: 0.9004 (mmm) cc_final: 0.8729 (mmt) REVERT: B 557 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8143 (mt) REVERT: B 569 TYR cc_start: 0.8927 (t80) cc_final: 0.8358 (t80) REVERT: B 670 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8448 (tm-30) REVERT: B 721 ASP cc_start: 0.8273 (p0) cc_final: 0.7457 (t0) REVERT: B 722 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8868 (pt) outliers start: 57 outliers final: 31 residues processed: 184 average time/residue: 0.0973 time to fit residues: 27.6533 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 : 0.432 ------------------------------------------------------------------------------- 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 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 409 ASP Chi-restraints excluded: chain A residue 455 LEU 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 750 MET Chi-restraints excluded: chain A residue 770 TYR 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 424 GLU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 567 CYS 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 848 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 122 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 696 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.099234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.073575 restraints weight = 29764.483| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.60 r_work: 0.2922 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12428 Z= 0.213 Angle : 0.592 8.983 16864 Z= 0.314 Chirality : 0.042 0.168 1836 Planarity : 0.005 0.068 2098 Dihedral : 6.795 89.151 1654 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 5.08 % Allowed : 20.18 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.22), residues: 1436 helix: 1.91 (0.16), residues: 900 sheet: -2.47 (0.51), residues: 76 loop : -0.97 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 701 TYR 0.028 0.002 TYR A 306 PHE 0.022 0.002 PHE B 852 TRP 0.012 0.001 TRP B 273 HIS 0.029 0.002 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00482 (12422) covalent geometry : angle 0.59182 (16852) SS BOND : bond 0.00317 ( 6) SS BOND : angle 1.14644 ( 12) hydrogen bonds : bond 0.05347 ( 720) hydrogen bonds : angle 4.38448 ( 2130) *********************** 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 198 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 131 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7042 (pm20) REVERT: A 243 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.8747 (tppp) REVERT: A 255 TYR cc_start: 0.7127 (m-80) cc_final: 0.6820 (m-80) REVERT: A 288 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8423 (tp) REVERT: A 409 ASP cc_start: 0.9152 (OUTLIER) cc_final: 0.8156 (t0) REVERT: A 417 GLU cc_start: 0.8955 (tp30) cc_final: 0.8418 (tp30) REVERT: A 534 MET cc_start: 0.8064 (mpt) cc_final: 0.7621 (mpt) REVERT: A 557 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8111 (mm) REVERT: A 661 LYS cc_start: 0.8921 (mtpp) cc_final: 0.8584 (mtpp) REVERT: A 684 SER cc_start: 0.9535 (t) cc_final: 0.9220 (p) REVERT: A 721 ASP cc_start: 0.8404 (p0) cc_final: 0.7611 (t0) REVERT: B 489 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6493 (mt) REVERT: B 555 MET cc_start: 0.9031 (mmm) cc_final: 0.8775 (mmt) REVERT: B 557 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8228 (mt) REVERT: B 569 TYR cc_start: 0.9077 (t80) cc_final: 0.8575 (t80) REVERT: B 601 CYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8241 (m) REVERT: B 670 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8586 (tm-30) REVERT: B 721 ASP cc_start: 0.8404 (p0) cc_final: 0.7478 (t0) outliers start: 67 outliers final: 43 residues processed: 180 average time/residue: 0.0963 time to fit residues: 26.5711 Evaluate side-chains 173 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 122 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 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 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 107 CYS Chi-restraints excluded: chain B residue 108 HIS 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 322 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 567 CYS Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 702 VAL 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 114 optimal weight: 4.9990 chunk 30 optimal weight: 0.0170 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 108 HIS B 696 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.101943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.076754 restraints weight = 29431.368| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.55 r_work: 0.2993 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12428 Z= 0.123 Angle : 0.522 7.248 16864 Z= 0.277 Chirality : 0.040 0.168 1836 Planarity : 0.005 0.069 2098 Dihedral : 6.640 89.484 1653 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.95 % Allowed : 21.32 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.22), residues: 1436 helix: 2.05 (0.17), residues: 894 sheet: -2.45 (0.50), residues: 66 loop : -1.05 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 649 TYR 0.024 0.001 TYR A 306 PHE 0.018 0.001 PHE B 852 TRP 0.011 0.001 TRP B 273 HIS 0.003 0.001 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00254 (12422) covalent geometry : angle 0.52188 (16852) SS BOND : bond 0.00351 ( 6) SS BOND : angle 0.94825 ( 12) hydrogen bonds : bond 0.04690 ( 720) hydrogen bonds : angle 4.27855 ( 2130) *********************** 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 191 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 139 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7095 (pm20) REVERT: A 243 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.8944 (tppp) REVERT: A 255 TYR cc_start: 0.7077 (m-80) cc_final: 0.6761 (m-80) REVERT: A 288 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8309 (tp) REVERT: A 409 ASP cc_start: 0.9113 (OUTLIER) cc_final: 0.8120 (t0) REVERT: A 417 GLU cc_start: 0.8956 (tp30) cc_final: 0.8389 (tp30) REVERT: A 534 MET cc_start: 0.7991 (mpt) cc_final: 0.7552 (mpt) REVERT: A 556 PHE cc_start: 0.9212 (t80) cc_final: 0.8944 (t80) REVERT: A 557 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7934 (mm) REVERT: A 661 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8575 (mtpp) REVERT: A 684 SER cc_start: 0.9536 (t) cc_final: 0.9213 (p) REVERT: A 721 ASP cc_start: 0.8316 (p0) cc_final: 0.7733 (t0) REVERT: B 489 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6499 (mt) REVERT: B 555 MET cc_start: 0.8948 (mmm) cc_final: 0.8667 (mmt) REVERT: B 557 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8113 (mt) REVERT: B 569 TYR cc_start: 0.9067 (t80) cc_final: 0.8502 (t80) REVERT: B 601 CYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8190 (m) REVERT: B 721 ASP cc_start: 0.8267 (p0) cc_final: 0.7552 (t0) outliers start: 52 outliers final: 33 residues processed: 177 average time/residue: 0.1037 time to fit residues: 27.6935 Evaluate side-chains 164 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 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 409 ASP Chi-restraints excluded: chain A residue 455 LEU 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 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 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 567 CYS Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 780 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 30 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 51 optimal weight: 0.0040 chunk 53 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- 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 108 HIS B 696 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.100842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.075357 restraints weight = 29554.887| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.56 r_work: 0.2958 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12428 Z= 0.153 Angle : 0.541 7.098 16864 Z= 0.288 Chirality : 0.041 0.210 1836 Planarity : 0.005 0.069 2098 Dihedral : 6.638 89.269 1653 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.10 % Allowed : 22.08 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.22), residues: 1436 helix: 2.03 (0.17), residues: 898 sheet: -2.54 (0.50), residues: 76 loop : -1.02 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 701 TYR 0.023 0.001 TYR A 569 PHE 0.025 0.001 PHE A 385 TRP 0.012 0.001 TRP B 273 HIS 0.008 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00337 (12422) covalent geometry : angle 0.54032 (16852) SS BOND : bond 0.00266 ( 6) SS BOND : angle 0.98819 ( 12) hydrogen bonds : bond 0.04852 ( 720) hydrogen bonds : angle 4.25834 ( 2130) *********************** 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 180 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 126 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7107 (pm20) REVERT: A 225 MET cc_start: 0.6625 (tpt) cc_final: 0.5496 (pmm) REVERT: A 243 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.8946 (tppp) REVERT: A 255 TYR cc_start: 0.7160 (m-80) cc_final: 0.6843 (m-80) REVERT: A 288 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8303 (tp) REVERT: A 409 ASP cc_start: 0.9097 (OUTLIER) cc_final: 0.8081 (t0) REVERT: A 417 GLU cc_start: 0.8907 (tp30) cc_final: 0.8364 (tp30) REVERT: A 534 MET cc_start: 0.7997 (mpt) cc_final: 0.7580 (mpt) REVERT: A 556 PHE cc_start: 0.9252 (t80) cc_final: 0.9013 (t80) REVERT: A 557 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7994 (mm) REVERT: A 661 LYS cc_start: 0.8872 (mtpp) cc_final: 0.8519 (mtpp) REVERT: A 684 SER cc_start: 0.9555 (t) cc_final: 0.9226 (p) REVERT: A 721 ASP cc_start: 0.8366 (p0) cc_final: 0.7740 (t0) REVERT: B 489 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6516 (mt) REVERT: B 555 MET cc_start: 0.8962 (mmm) cc_final: 0.8674 (mmt) REVERT: B 557 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8081 (mm) REVERT: B 569 TYR cc_start: 0.9085 (t80) cc_final: 0.8508 (t80) REVERT: B 601 CYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8196 (m) REVERT: B 721 ASP cc_start: 0.8377 (p0) cc_final: 0.7642 (t0) outliers start: 54 outliers final: 36 residues processed: 168 average time/residue: 0.0983 time to fit residues: 25.1259 Evaluate side-chains 166 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 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 409 ASP Chi-restraints excluded: chain A residue 455 LEU 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 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 145 LYS Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 322 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 567 CYS Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 702 VAL 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 118 optimal weight: 0.0970 chunk 71 optimal weight: 0.0040 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 109 optimal weight: 0.1980 overall best weight: 0.3590 ------------------------------------------------------------------------------- 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 674 GLN B 696 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.104676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.079515 restraints weight = 29265.162| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.67 r_work: 0.3015 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12428 Z= 0.112 Angle : 0.521 7.470 16864 Z= 0.274 Chirality : 0.040 0.215 1836 Planarity : 0.005 0.070 2098 Dihedral : 6.573 89.798 1653 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.11 % Allowed : 23.22 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.22), residues: 1436 helix: 2.12 (0.17), residues: 896 sheet: -2.36 (0.51), residues: 66 loop : -1.10 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 649 TYR 0.022 0.001 TYR A 569 PHE 0.025 0.001 PHE B 852 TRP 0.011 0.001 TRP A 397 HIS 0.002 0.000 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00224 (12422) covalent geometry : angle 0.52020 (16852) SS BOND : bond 0.00076 ( 6) SS BOND : angle 0.85150 ( 12) hydrogen bonds : bond 0.04418 ( 720) hydrogen bonds : angle 4.21166 ( 2130) *********************** 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 186 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7038 (pm20) REVERT: A 143 HIS cc_start: 0.8947 (m90) cc_final: 0.8703 (m90) REVERT: A 225 MET cc_start: 0.6627 (tpt) cc_final: 0.5597 (pmm) REVERT: A 243 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8990 (tppp) REVERT: A 255 TYR cc_start: 0.7130 (m-80) cc_final: 0.6775 (m-80) REVERT: A 288 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8287 (tp) REVERT: A 409 ASP cc_start: 0.9007 (OUTLIER) cc_final: 0.7947 (t0) REVERT: A 417 GLU cc_start: 0.8998 (tp30) cc_final: 0.8424 (tp30) REVERT: A 534 MET cc_start: 0.7881 (mpt) cc_final: 0.7444 (mpt) REVERT: A 556 PHE cc_start: 0.9178 (t80) cc_final: 0.8925 (t80) REVERT: A 557 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7901 (mm) REVERT: A 661 LYS cc_start: 0.8850 (mtpp) cc_final: 0.8484 (mtpp) REVERT: A 684 SER cc_start: 0.9537 (t) cc_final: 0.9196 (p) REVERT: A 721 ASP cc_start: 0.8279 (p0) cc_final: 0.7805 (t0) REVERT: B 306 TYR cc_start: 0.9051 (t80) cc_final: 0.8828 (t80) REVERT: B 489 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6603 (mt) REVERT: B 555 MET cc_start: 0.8870 (mmm) cc_final: 0.8565 (mmt) REVERT: B 557 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7987 (mm) REVERT: B 569 TYR cc_start: 0.9019 (t80) cc_final: 0.8400 (t80) REVERT: B 601 CYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8127 (m) REVERT: B 721 ASP cc_start: 0.8324 (p0) cc_final: 0.7714 (t0) outliers start: 41 outliers final: 29 residues processed: 177 average time/residue: 0.0906 time to fit residues: 24.6586 Evaluate side-chains 171 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 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 409 ASP Chi-restraints excluded: chain A residue 455 LEU 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 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 62 LEU Chi-restraints excluded: chain B residue 73 PHE 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 318 VAL 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 677 PHE Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN B 696 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.099073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.074025 restraints weight = 29624.394| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.46 r_work: 0.2942 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12428 Z= 0.205 Angle : 0.586 6.850 16864 Z= 0.312 Chirality : 0.042 0.208 1836 Planarity : 0.005 0.069 2098 Dihedral : 6.654 89.604 1653 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.57 % Allowed : 22.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.22), residues: 1436 helix: 2.02 (0.17), residues: 900 sheet: -2.41 (0.51), residues: 76 loop : -0.99 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 701 TYR 0.027 0.002 TYR A 569 PHE 0.026 0.002 PHE B 852 TRP 0.013 0.001 TRP B 273 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00462 (12422) covalent geometry : angle 0.58551 (16852) SS BOND : bond 0.00349 ( 6) SS BOND : angle 1.02785 ( 12) hydrogen bonds : bond 0.05076 ( 720) hydrogen bonds : angle 4.27394 ( 2130) *********************** 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 170 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 123 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7156 (pm20) REVERT: A 225 MET cc_start: 0.6865 (tpt) cc_final: 0.5803 (pmm) REVERT: A 243 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.8951 (tppp) REVERT: A 255 TYR cc_start: 0.7240 (m-80) cc_final: 0.6955 (m-80) REVERT: A 409 ASP cc_start: 0.9091 (OUTLIER) cc_final: 0.8072 (t0) REVERT: A 417 GLU cc_start: 0.8884 (tp30) cc_final: 0.8366 (tp30) REVERT: A 534 MET cc_start: 0.7939 (mpt) cc_final: 0.7559 (mpt) REVERT: A 557 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8024 (mm) REVERT: A 684 SER cc_start: 0.9565 (t) cc_final: 0.9219 (p) REVERT: A 721 ASP cc_start: 0.8431 (p0) cc_final: 0.7802 (t0) REVERT: B 555 MET cc_start: 0.8996 (mmm) cc_final: 0.8688 (mmt) REVERT: B 557 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8121 (mm) REVERT: B 569 TYR cc_start: 0.9081 (t80) cc_final: 0.8477 (t80) REVERT: B 601 CYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8193 (m) REVERT: B 721 ASP cc_start: 0.8408 (p0) cc_final: 0.7695 (t0) outliers start: 47 outliers final: 35 residues processed: 157 average time/residue: 0.0982 time to fit residues: 23.5811 Evaluate side-chains 163 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 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 322 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 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 145 LYS Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 318 VAL 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 557 LEU Chi-restraints excluded: chain B residue 601 CYS 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 126 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 9 optimal weight: 0.0670 chunk 41 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- 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 696 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.101584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.076314 restraints weight = 29369.269| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.52 r_work: 0.2986 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12428 Z= 0.130 Angle : 0.541 7.127 16864 Z= 0.287 Chirality : 0.041 0.208 1836 Planarity : 0.005 0.069 2098 Dihedral : 6.593 89.578 1653 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.26 % Allowed : 23.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.22), residues: 1436 helix: 2.12 (0.17), residues: 892 sheet: -2.31 (0.51), residues: 66 loop : -1.10 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 649 TYR 0.026 0.001 TYR A 569 PHE 0.029 0.002 PHE A 385 TRP 0.011 0.001 TRP B 273 HIS 0.002 0.001 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00278 (12422) covalent geometry : angle 0.54017 (16852) SS BOND : bond 0.00172 ( 6) SS BOND : angle 0.96201 ( 12) hydrogen bonds : bond 0.04691 ( 720) hydrogen bonds : angle 4.21764 ( 2130) ********************** 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 176 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7096 (pm20) REVERT: A 143 HIS cc_start: 0.8972 (m90) cc_final: 0.8726 (m90) REVERT: A 225 MET cc_start: 0.6697 (tpt) cc_final: 0.5736 (pmm) REVERT: A 243 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.8982 (tppp) REVERT: A 255 TYR cc_start: 0.7248 (m-80) cc_final: 0.6991 (m-80) REVERT: A 409 ASP cc_start: 0.8992 (OUTLIER) cc_final: 0.8010 (t0) REVERT: A 414 GLN cc_start: 0.8437 (mp10) cc_final: 0.8186 (mm110) REVERT: A 417 GLU cc_start: 0.8958 (tp30) cc_final: 0.8413 (tp30) REVERT: A 534 MET cc_start: 0.7875 (mpt) cc_final: 0.7515 (mpt) REVERT: A 557 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7972 (mm) REVERT: A 684 SER cc_start: 0.9555 (t) cc_final: 0.9210 (p) REVERT: A 721 ASP cc_start: 0.8316 (p0) cc_final: 0.7796 (t0) REVERT: B 555 MET cc_start: 0.8924 (mmm) cc_final: 0.8606 (mmt) REVERT: B 557 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8028 (mm) REVERT: B 569 TYR cc_start: 0.9063 (t80) cc_final: 0.8388 (t80) REVERT: B 601 CYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8144 (m) REVERT: B 721 ASP cc_start: 0.8395 (p0) cc_final: 0.7766 (t0) outliers start: 43 outliers final: 34 residues processed: 162 average time/residue: 0.0934 time to fit residues: 23.2281 Evaluate side-chains 167 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 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 322 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 455 LEU 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 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 145 LYS 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 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 557 LEU Chi-restraints excluded: chain B residue 601 CYS 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 101 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 138 optimal weight: 0.0570 chunk 129 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.102052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.076868 restraints weight = 29248.740| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.51 r_work: 0.2996 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12428 Z= 0.130 Angle : 0.546 7.527 16864 Z= 0.288 Chirality : 0.041 0.221 1836 Planarity : 0.005 0.069 2098 Dihedral : 6.546 89.662 1653 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.11 % Allowed : 23.67 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.22), residues: 1436 helix: 2.13 (0.17), residues: 890 sheet: -2.36 (0.51), residues: 76 loop : -1.09 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 649 TYR 0.026 0.001 TYR A 569 PHE 0.030 0.002 PHE A 556 TRP 0.010 0.001 TRP B 273 HIS 0.002 0.001 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00276 (12422) covalent geometry : angle 0.54590 (16852) SS BOND : bond 0.00156 ( 6) SS BOND : angle 0.91790 ( 12) hydrogen bonds : bond 0.04620 ( 720) hydrogen bonds : angle 4.19709 ( 2130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2706.89 seconds wall clock time: 47 minutes 19.10 seconds (2839.10 seconds total)