Starting phenix.real_space_refine on Wed Jul 30 08:25:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b8g_15913/07_2025/8b8g_15913.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b8g_15913/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8b8g_15913/07_2025/8b8g_15913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b8g_15913/07_2025/8b8g_15913.map" model { file = "/net/cci-nas-00/data/ceres_data/8b8g_15913/07_2025/8b8g_15913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b8g_15913/07_2025/8b8g_15913.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 7946 2.51 5 N 1944 2.21 5 O 2116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12086 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 6043 Classifications: {'peptide': 732} Link IDs: {'PTRANS': 34, 'TRANS': 697} Chain breaks: 6 Restraints were copied for chains: B Time building chain proxies: 13.10, per 1000 atoms: 1.08 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: 3.02 Conformation dependent library (CDL) restraints added in 1.6 seconds 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2788 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 64.1% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 91 through 109 Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.742A pdb=" N PHE A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 294 through 327 Processing helix chain 'A' and resid 331 through 338 removed outlier: 3.919A pdb=" N LYS A 335 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N CYS A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.541A pdb=" N GLN A 345 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 346' Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.732A pdb=" N ILE A 363 " --> pdb=" O ARG A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 376 through 409 removed outlier: 3.561A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 Processing helix chain 'A' and resid 448 through 489 removed outlier: 3.748A pdb=" N THR A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 539 removed outlier: 3.970A pdb=" N LYS A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 572 removed outlier: 4.107A pdb=" N ILE A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 636 Proline residue: A 628 - end of helix removed outlier: 3.595A pdb=" N GLY A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 removed outlier: 3.502A pdb=" N HIS A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 681 removed outlier: 3.877A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 685 Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.524A pdb=" N LEU A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 747 removed outlier: 3.916A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 759 Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.828A pdb=" N LEU A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'A' and resid 861 through 877 Processing helix chain 'B' and resid 91 through 109 Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.742A pdb=" N PHE B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 233 through 240 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 284 through 291 Processing helix chain 'B' and resid 294 through 327 Processing helix chain 'B' and resid 331 through 338 removed outlier: 3.919A pdb=" N LYS B 335 " --> pdb=" O CYS B 331 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N CYS B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 346 removed outlier: 3.541A pdb=" N GLN B 345 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 346 " --> pdb=" O GLY B 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 342 through 346' Processing helix chain 'B' and resid 360 through 363 removed outlier: 3.732A pdb=" N ILE B 363 " --> pdb=" O ARG B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 364 through 372 Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.561A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 427 Processing helix chain 'B' and resid 448 through 489 removed outlier: 3.748A pdb=" N THR B 487 " --> pdb=" O ILE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 539 removed outlier: 3.970A pdb=" N LYS B 530 " --> pdb=" O THR B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 572 removed outlier: 4.106A pdb=" N ILE B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 636 Proline residue: B 628 - end of helix removed outlier: 3.595A pdb=" N GLY B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG B 636 " --> pdb=" O ASN B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 655 removed outlier: 3.503A pdb=" N HIS B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 681 removed outlier: 3.877A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 685 Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.524A pdb=" N LEU B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 3.916A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 759 Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.828A pdb=" N LEU B 781 " --> pdb=" O ILE B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 877 Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 116 Processing sheet with id=AA2, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AA3, first strand: chain 'B' and resid 111 through 116 Processing sheet with id=AA4, first strand: chain 'B' and resid 784 through 785 720 hydrogen bonds defined for protein. 2130 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.50 Time building geometry restraints manager: 3.60 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: 0.06 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: 1.820 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 35.320 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.960 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.23), residues: 1436 helix: 1.72 (0.17), residues: 880 sheet: -2.17 (0.52), residues: 76 loop : -1.10 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 397 HIS 0.002 0.001 HIS B 249 PHE 0.014 0.001 PHE B 560 TYR 0.015 0.001 TYR B 306 ARG 0.002 0.000 ARG B 808 Details of bonding type rmsd hydrogen bonds : bond 0.12148 ( 720) hydrogen bonds : angle 5.23664 ( 2130) SS BOND : bond 0.00445 ( 6) SS BOND : angle 1.84431 ( 12) covalent geometry : bond 0.00430 (12422) covalent geometry : angle 0.55565 (16852) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 183 time to evaluate : 1.258 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: 0.2323 time to fit residues: 91.0656 Evaluate side-chains 161 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 823 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN A 720 GLN B 621 ASN B 696 ASN B 710 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.100484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.075144 restraints weight = 28970.627| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.40 r_work: 0.2970 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12428 Z= 0.181 Angle : 0.601 10.855 16864 Z= 0.315 Chirality : 0.041 0.178 1836 Planarity : 0.005 0.067 2098 Dihedral : 8.571 87.425 1699 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 5.16 % Allowed : 16.01 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.22), residues: 1436 helix: 1.78 (0.17), residues: 898 sheet: -2.21 (0.54), residues: 76 loop : -0.92 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 397 HIS 0.003 0.001 HIS A 768 PHE 0.020 0.002 PHE B 852 TYR 0.016 0.002 TYR B 569 ARG 0.003 0.000 ARG B 266 Details of bonding type rmsd hydrogen bonds : bond 0.05431 ( 720) hydrogen bonds : angle 4.53300 ( 2130) SS BOND : bond 0.00236 ( 6) SS BOND : angle 1.22216 ( 12) covalent geometry : bond 0.00401 (12422) covalent geometry : angle 0.60048 (16852) *********************** 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 210 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 142 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.7995 (mpt180) cc_final: 0.7467 (mpt180) REVERT: A 78 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7028 (pm20) REVERT: A 113 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7333 (pm20) REVERT: A 243 LYS cc_start: 0.9444 (OUTLIER) cc_final: 0.8586 (tppp) REVERT: A 385 PHE cc_start: 0.9211 (t80) cc_final: 0.8983 (t80) REVERT: A 404 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8212 (mm) REVERT: A 409 ASP cc_start: 0.9140 (OUTLIER) cc_final: 0.8197 (t0) REVERT: A 417 GLU cc_start: 0.9011 (tp30) cc_final: 0.8400 (tp30) REVERT: A 534 MET cc_start: 0.7925 (mpt) cc_final: 0.7441 (mpt) REVERT: A 557 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8041 (mt) REVERT: A 661 LYS cc_start: 0.8862 (mtpp) cc_final: 0.8476 (mtpp) REVERT: A 721 ASP cc_start: 0.8322 (p0) cc_final: 0.7420 (t0) REVERT: A 773 MET cc_start: 0.9362 (mmm) cc_final: 0.9061 (mmm) REVERT: B 125 PHE cc_start: 0.8812 (m-80) cc_final: 0.8435 (m-10) REVERT: B 255 TYR cc_start: 0.7263 (m-80) cc_final: 0.7049 (m-80) REVERT: B 371 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8641 (tt) REVERT: B 417 GLU cc_start: 0.9026 (tp30) cc_final: 0.8435 (tp30) REVERT: B 462 PHE cc_start: 0.8546 (t80) cc_final: 0.8345 (t80) REVERT: B 489 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6799 (mt) REVERT: B 555 MET cc_start: 0.8977 (mmm) cc_final: 0.8703 (mmt) REVERT: B 557 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8153 (mt) REVERT: B 721 ASP cc_start: 0.8367 (p0) cc_final: 0.7358 (t0) outliers start: 68 outliers final: 36 residues processed: 200 average time/residue: 0.2001 time to fit residues: 60.9453 Evaluate side-chains 166 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 107 CYS Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 3 optimal weight: 0.2980 chunk 77 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 104 optimal weight: 0.3980 chunk 63 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 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 = 0.102689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.077522 restraints weight = 29275.991| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.58 r_work: 0.3008 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2182 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 : 0.538 9.220 16864 Z= 0.282 Chirality : 0.040 0.174 1836 Planarity : 0.005 0.069 2098 Dihedral : 7.939 88.799 1676 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.02 % Allowed : 17.30 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.22), residues: 1436 helix: 1.92 (0.16), residues: 896 sheet: -2.30 (0.53), residues: 76 loop : -1.00 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 397 HIS 0.002 0.000 HIS A 768 PHE 0.019 0.001 PHE B 852 TYR 0.014 0.001 TYR A 569 ARG 0.002 0.000 ARG B 649 Details of bonding type rmsd hydrogen bonds : bond 0.04862 ( 720) hydrogen bonds : angle 4.35816 ( 2130) SS BOND : bond 0.00212 ( 6) SS BOND : angle 0.88047 ( 12) covalent geometry : bond 0.00253 (12422) covalent geometry : angle 0.53740 (16852) *********************** 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: 53 poor density : 145 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7125 (pm20) REVERT: A 243 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.8850 (tppp) REVERT: A 255 TYR cc_start: 0.7125 (m-80) cc_final: 0.6803 (m-80) REVERT: A 385 PHE cc_start: 0.9217 (t80) cc_final: 0.8990 (t80) REVERT: A 404 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8322 (mm) REVERT: A 409 ASP cc_start: 0.9144 (OUTLIER) cc_final: 0.8161 (t0) REVERT: A 417 GLU cc_start: 0.8966 (tp30) cc_final: 0.8448 (tp30) REVERT: A 534 MET cc_start: 0.7911 (mpt) cc_final: 0.7396 (mpt) REVERT: A 556 PHE cc_start: 0.9217 (t80) cc_final: 0.8939 (t80) REVERT: A 557 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7940 (mm) REVERT: A 661 LYS cc_start: 0.8819 (mtpp) cc_final: 0.8472 (mtpp) REVERT: A 684 SER cc_start: 0.9489 (t) cc_final: 0.9150 (p) REVERT: A 721 ASP cc_start: 0.8355 (p0) cc_final: 0.7736 (t0) REVERT: A 773 MET cc_start: 0.9443 (mmm) cc_final: 0.9223 (tpp) REVERT: B 125 PHE cc_start: 0.8724 (m-80) cc_final: 0.8438 (m-10) REVERT: B 371 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8594 (tt) REVERT: B 489 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6480 (mt) REVERT: B 555 MET cc_start: 0.8992 (mmm) cc_final: 0.8715 (mmt) REVERT: B 557 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8141 (mt) REVERT: B 569 TYR cc_start: 0.8935 (t80) cc_final: 0.8379 (t80) REVERT: B 670 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8488 (tm-30) REVERT: B 721 ASP cc_start: 0.8301 (p0) cc_final: 0.7462 (t0) REVERT: B 722 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8848 (pt) outliers start: 53 outliers final: 28 residues processed: 190 average time/residue: 0.2343 time to fit residues: 68.2319 Evaluate side-chains 163 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 2.126 ------------------------------------------------------------------------------- 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 228 VAL Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain 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 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 722 ILE Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 78 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 46 optimal weight: 0.0570 chunk 13 optimal weight: 1.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- 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 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.100375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.075186 restraints weight = 29417.027| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.51 r_work: 0.2965 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12428 Z= 0.166 Angle : 0.550 8.985 16864 Z= 0.293 Chirality : 0.041 0.166 1836 Planarity : 0.005 0.069 2098 Dihedral : 7.404 88.916 1663 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.78 % Allowed : 17.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.22), residues: 1436 helix: 1.89 (0.16), residues: 896 sheet: -2.37 (0.52), residues: 76 loop : -0.96 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.003 0.001 HIS B 768 PHE 0.020 0.002 PHE B 852 TYR 0.029 0.001 TYR A 306 ARG 0.002 0.000 ARG A 701 Details of bonding type rmsd hydrogen bonds : bond 0.05080 ( 720) hydrogen bonds : angle 4.34828 ( 2130) SS BOND : bond 0.00248 ( 6) SS BOND : angle 0.96345 ( 12) covalent geometry : bond 0.00369 (12422) covalent geometry : angle 0.54952 (16852) *********************** 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 194 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 131 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7156 (pm20) REVERT: A 243 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.8815 (tppp) REVERT: A 255 TYR cc_start: 0.7149 (m-80) cc_final: 0.6830 (m-80) REVERT: A 371 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8715 (tt) REVERT: A 404 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8389 (mm) REVERT: A 409 ASP cc_start: 0.9146 (OUTLIER) cc_final: 0.8150 (t0) REVERT: A 417 GLU cc_start: 0.8965 (tp30) cc_final: 0.8435 (tp30) REVERT: A 534 MET cc_start: 0.7989 (mpt) cc_final: 0.7532 (mpt) REVERT: A 557 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8029 (mm) REVERT: A 631 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8050 (mpt) REVERT: A 661 LYS cc_start: 0.8847 (mtpp) cc_final: 0.8455 (mtpp) REVERT: A 684 SER cc_start: 0.9538 (t) cc_final: 0.9214 (p) REVERT: A 721 ASP cc_start: 0.8392 (p0) cc_final: 0.7683 (t0) REVERT: B 125 PHE cc_start: 0.8802 (m-80) cc_final: 0.8550 (m-10) REVERT: B 371 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8598 (tt) REVERT: B 489 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6602 (mt) REVERT: B 555 MET cc_start: 0.8990 (mmm) cc_final: 0.8744 (mmt) REVERT: B 557 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8175 (mt) REVERT: B 569 TYR cc_start: 0.9006 (t80) cc_final: 0.8413 (t80) REVERT: B 671 MET cc_start: 0.9453 (tpp) cc_final: 0.9232 (mmt) REVERT: B 721 ASP cc_start: 0.8347 (p0) cc_final: 0.7441 (t0) REVERT: B 842 MET cc_start: 0.9051 (ttp) cc_final: 0.8802 (ttp) outliers start: 63 outliers final: 39 residues processed: 180 average time/residue: 0.2076 time to fit residues: 56.6037 Evaluate side-chains 171 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 122 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 287 LEU 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 371 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 823 LYS 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 91 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 49 optimal weight: 0.0170 overall best weight: 1.3622 ------------------------------------------------------------------------------- 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 351 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 = 0.3586 r_free = 0.3586 target = 0.100213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.074541 restraints weight = 29329.693| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.59 r_work: 0.2941 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12428 Z= 0.176 Angle : 0.556 8.421 16864 Z= 0.297 Chirality : 0.041 0.189 1836 Planarity : 0.005 0.069 2098 Dihedral : 7.455 89.348 1663 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.61 % Allowed : 18.97 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.22), residues: 1436 helix: 1.85 (0.16), residues: 900 sheet: -2.50 (0.52), residues: 76 loop : -0.99 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 705 HIS 0.003 0.001 HIS B 768 PHE 0.027 0.002 PHE A 385 TYR 0.027 0.002 TYR A 306 ARG 0.002 0.000 ARG B 701 Details of bonding type rmsd hydrogen bonds : bond 0.05142 ( 720) hydrogen bonds : angle 4.35687 ( 2130) SS BOND : bond 0.00219 ( 6) SS BOND : angle 1.07438 ( 12) covalent geometry : bond 0.00391 (12422) covalent geometry : angle 0.55530 (16852) *********************** 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 206 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 132 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7142 (pm20) REVERT: A 113 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6990 (pm20) REVERT: A 243 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.8796 (tppp) REVERT: A 255 TYR cc_start: 0.7129 (m-80) cc_final: 0.6834 (m-80) REVERT: A 371 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8681 (tt) REVERT: A 404 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8427 (mm) REVERT: A 409 ASP cc_start: 0.9154 (OUTLIER) cc_final: 0.8156 (t0) REVERT: A 417 GLU cc_start: 0.8949 (tp30) cc_final: 0.8407 (tp30) REVERT: A 534 MET cc_start: 0.8015 (mpt) cc_final: 0.7603 (mpt) REVERT: A 557 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8059 (mm) REVERT: A 631 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7779 (mpt) REVERT: A 661 LYS cc_start: 0.8874 (mtpp) cc_final: 0.8513 (mtpp) REVERT: A 684 SER cc_start: 0.9577 (t) cc_final: 0.9241 (p) REVERT: A 721 ASP cc_start: 0.8354 (p0) cc_final: 0.7683 (t0) REVERT: A 773 MET cc_start: 0.9380 (mmm) cc_final: 0.9140 (mmm) REVERT: B 371 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8762 (tt) REVERT: B 489 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6650 (mt) REVERT: B 555 MET cc_start: 0.9015 (mmm) cc_final: 0.8745 (mmt) REVERT: B 557 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8159 (mm) REVERT: B 569 TYR cc_start: 0.9059 (t80) cc_final: 0.8593 (t80) REVERT: B 601 CYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8260 (m) REVERT: B 717 GLU cc_start: 0.8706 (mp0) cc_final: 0.8449 (mp0) REVERT: B 721 ASP cc_start: 0.8313 (p0) cc_final: 0.7562 (t0) outliers start: 74 outliers final: 44 residues processed: 188 average time/residue: 0.2284 time to fit residues: 64.0622 Evaluate side-chains 176 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 120 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 287 LEU 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 371 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 722 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 220 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 ILE 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 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 142 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 90 optimal weight: 0.1980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.100434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.075452 restraints weight = 29817.648| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.49 r_work: 0.2971 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2915 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= 0.144 Angle : 0.537 7.950 16864 Z= 0.287 Chirality : 0.041 0.191 1836 Planarity : 0.005 0.070 2098 Dihedral : 7.349 89.606 1662 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.55 % Allowed : 21.24 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.22), residues: 1436 helix: 1.90 (0.17), residues: 900 sheet: -2.45 (0.52), residues: 76 loop : -1.02 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 273 HIS 0.002 0.001 HIS B 768 PHE 0.027 0.001 PHE A 385 TYR 0.024 0.001 TYR A 306 ARG 0.002 0.000 ARG B 649 Details of bonding type rmsd hydrogen bonds : bond 0.04923 ( 720) hydrogen bonds : angle 4.31916 ( 2130) SS BOND : bond 0.00186 ( 6) SS BOND : angle 0.93786 ( 12) covalent geometry : bond 0.00314 (12422) covalent geometry : angle 0.53651 (16852) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 132 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7122 (pm20) REVERT: A 243 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.8915 (tppp) REVERT: A 255 TYR cc_start: 0.7143 (m-80) cc_final: 0.6853 (m-80) REVERT: A 371 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8653 (tt) REVERT: A 404 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8432 (mm) REVERT: A 409 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8102 (t0) REVERT: A 417 GLU cc_start: 0.8929 (tp30) cc_final: 0.8395 (tp30) REVERT: A 534 MET cc_start: 0.7970 (mpt) cc_final: 0.7561 (mpt) REVERT: A 556 PHE cc_start: 0.9269 (t80) cc_final: 0.8972 (t80) REVERT: A 557 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7977 (mm) REVERT: A 661 LYS cc_start: 0.8869 (mtpp) cc_final: 0.8534 (mtpp) REVERT: A 684 SER cc_start: 0.9573 (t) cc_final: 0.9233 (p) REVERT: A 721 ASP cc_start: 0.8358 (p0) cc_final: 0.7749 (t0) REVERT: B 371 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8764 (tt) REVERT: B 489 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6629 (mt) REVERT: B 555 MET cc_start: 0.8949 (mmm) cc_final: 0.8665 (mmt) REVERT: B 557 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8087 (mm) REVERT: B 569 TYR cc_start: 0.9082 (t80) cc_final: 0.8551 (t80) REVERT: B 601 CYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8234 (m) REVERT: B 721 ASP cc_start: 0.8290 (p0) cc_final: 0.7558 (t0) outliers start: 60 outliers final: 41 residues processed: 178 average time/residue: 0.2582 time to fit residues: 69.4471 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 : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 722 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 220 VAL Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 91 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.100922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.075676 restraints weight = 29705.442| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.51 r_work: 0.2974 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3069 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= 0.139 Angle : 0.536 7.115 16864 Z= 0.287 Chirality : 0.041 0.199 1836 Planarity : 0.005 0.070 2098 Dihedral : 7.217 89.545 1660 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.55 % Allowed : 21.32 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.22), residues: 1436 helix: 1.95 (0.17), residues: 898 sheet: -2.45 (0.52), residues: 76 loop : -1.06 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 705 HIS 0.003 0.001 HIS B 108 PHE 0.025 0.001 PHE B 852 TYR 0.023 0.001 TYR A 306 ARG 0.002 0.000 ARG A 701 Details of bonding type rmsd hydrogen bonds : bond 0.04823 ( 720) hydrogen bonds : angle 4.29681 ( 2130) SS BOND : bond 0.00209 ( 6) SS BOND : angle 0.98935 ( 12) covalent geometry : bond 0.00301 (12422) covalent geometry : angle 0.53578 (16852) *********************** 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 194 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 134 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7084 (pm20) REVERT: A 225 MET cc_start: 0.6693 (tpt) cc_final: 0.5554 (pmm) REVERT: A 243 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8916 (tppp) REVERT: A 255 TYR cc_start: 0.7162 (m-80) cc_final: 0.6906 (m-80) REVERT: A 371 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8645 (tt) REVERT: A 404 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8384 (mm) REVERT: A 409 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8076 (t0) REVERT: A 417 GLU cc_start: 0.8954 (tp30) cc_final: 0.8409 (tp30) REVERT: A 534 MET cc_start: 0.7930 (mpt) cc_final: 0.7545 (mpt) REVERT: A 556 PHE cc_start: 0.9233 (t80) cc_final: 0.8951 (t80) REVERT: A 557 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7977 (mm) REVERT: A 661 LYS cc_start: 0.8874 (mtpp) cc_final: 0.8535 (mtpp) REVERT: A 684 SER cc_start: 0.9575 (t) cc_final: 0.9226 (p) REVERT: A 721 ASP cc_start: 0.8353 (p0) cc_final: 0.7760 (t0) REVERT: B 371 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8687 (tt) REVERT: B 489 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6517 (mt) REVERT: B 555 MET cc_start: 0.8917 (mmm) cc_final: 0.8615 (mmt) REVERT: B 557 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8085 (mm) REVERT: B 569 TYR cc_start: 0.9087 (t80) cc_final: 0.8499 (t80) REVERT: B 601 CYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8213 (m) REVERT: B 721 ASP cc_start: 0.8368 (p0) cc_final: 0.7712 (t0) outliers start: 60 outliers final: 43 residues processed: 179 average time/residue: 0.2150 time to fit residues: 58.0827 Evaluate side-chains 178 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 125 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 722 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 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 371 LEU Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 696 ASN 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 120 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 142 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 85 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 ASN B 108 HIS B 696 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.099063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.073988 restraints weight = 29913.482| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.44 r_work: 0.2943 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12428 Z= 0.194 Angle : 0.578 7.040 16864 Z= 0.308 Chirality : 0.042 0.203 1836 Planarity : 0.005 0.069 2098 Dihedral : 7.263 89.328 1660 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.63 % Allowed : 22.08 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.22), residues: 1436 helix: 1.92 (0.17), residues: 900 sheet: -2.47 (0.52), residues: 76 loop : -1.07 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 273 HIS 0.004 0.001 HIS B 108 PHE 0.026 0.002 PHE B 852 TYR 0.024 0.002 TYR A 306 ARG 0.002 0.000 ARG A 701 Details of bonding type rmsd hydrogen bonds : bond 0.05108 ( 720) hydrogen bonds : angle 4.35781 ( 2130) SS BOND : bond 0.00392 ( 6) SS BOND : angle 1.06223 ( 12) covalent geometry : bond 0.00435 (12422) covalent geometry : angle 0.57786 (16852) *********************** 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 185 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 124 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7123 (pm20) REVERT: A 113 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6624 (pm20) REVERT: A 225 MET cc_start: 0.7015 (tpt) cc_final: 0.5749 (pmm) REVERT: A 243 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8787 (tppp) REVERT: A 255 TYR cc_start: 0.7185 (m-80) cc_final: 0.6944 (m-80) REVERT: A 371 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8675 (tt) REVERT: A 404 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8387 (mm) REVERT: A 409 ASP cc_start: 0.9095 (OUTLIER) cc_final: 0.8098 (t0) REVERT: A 414 GLN cc_start: 0.8561 (mp10) cc_final: 0.8257 (mp10) REVERT: A 417 GLU cc_start: 0.8935 (tp30) cc_final: 0.8400 (tp30) REVERT: A 534 MET cc_start: 0.7897 (mpt) cc_final: 0.7494 (mpt) REVERT: A 557 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7992 (mm) REVERT: A 661 LYS cc_start: 0.8956 (mtpp) cc_final: 0.8631 (mtpp) REVERT: A 684 SER cc_start: 0.9589 (t) cc_final: 0.9241 (p) REVERT: A 721 ASP cc_start: 0.8355 (p0) cc_final: 0.7704 (t0) REVERT: B 371 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8727 (tt) REVERT: B 555 MET cc_start: 0.8963 (mmm) cc_final: 0.8653 (mmt) REVERT: B 557 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8099 (mm) REVERT: B 569 TYR cc_start: 0.9129 (t80) cc_final: 0.8575 (t80) REVERT: B 601 CYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8242 (m) REVERT: B 721 ASP cc_start: 0.8431 (p0) cc_final: 0.7719 (t0) outliers start: 61 outliers final: 47 residues processed: 170 average time/residue: 0.2131 time to fit residues: 54.7257 Evaluate side-chains 177 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 120 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 722 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 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 322 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 823 LYS Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 100 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.100726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.075631 restraints weight = 29371.487| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.44 r_work: 0.2971 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12428 Z= 0.135 Angle : 0.551 6.958 16864 Z= 0.293 Chirality : 0.041 0.205 1836 Planarity : 0.005 0.069 2098 Dihedral : 7.238 89.718 1660 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.10 % Allowed : 22.46 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.22), residues: 1436 helix: 1.98 (0.17), residues: 898 sheet: -2.42 (0.52), residues: 76 loop : -1.06 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 273 HIS 0.005 0.001 HIS B 108 PHE 0.028 0.001 PHE A 385 TYR 0.023 0.001 TYR A 306 ARG 0.002 0.000 ARG A 753 Details of bonding type rmsd hydrogen bonds : bond 0.04842 ( 720) hydrogen bonds : angle 4.30830 ( 2130) SS BOND : bond 0.00159 ( 6) SS BOND : angle 0.96365 ( 12) covalent geometry : bond 0.00287 (12422) covalent geometry : angle 0.55055 (16852) *********************** 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 183 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 129 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7115 (pm20) REVERT: A 225 MET cc_start: 0.6930 (tpt) cc_final: 0.5768 (pmm) REVERT: A 243 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.8902 (tppp) REVERT: A 255 TYR cc_start: 0.7157 (m-80) cc_final: 0.6898 (m-80) REVERT: A 371 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8623 (tt) REVERT: A 404 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8407 (mm) REVERT: A 409 ASP cc_start: 0.9088 (OUTLIER) cc_final: 0.8091 (t0) REVERT: A 414 GLN cc_start: 0.8579 (mp10) cc_final: 0.8266 (mp10) REVERT: A 417 GLU cc_start: 0.8953 (tp30) cc_final: 0.8409 (tp30) REVERT: A 534 MET cc_start: 0.7865 (mpt) cc_final: 0.7480 (mpt) REVERT: A 556 PHE cc_start: 0.9251 (t80) cc_final: 0.8974 (t80) REVERT: A 557 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7942 (mm) REVERT: A 661 LYS cc_start: 0.8979 (mtpp) cc_final: 0.8621 (mtpp) REVERT: A 684 SER cc_start: 0.9581 (t) cc_final: 0.9221 (p) REVERT: A 721 ASP cc_start: 0.8365 (p0) cc_final: 0.7763 (t0) REVERT: B 371 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8679 (tt) REVERT: B 555 MET cc_start: 0.8973 (mmm) cc_final: 0.8684 (mmt) REVERT: B 557 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8037 (mm) REVERT: B 569 TYR cc_start: 0.9110 (t80) cc_final: 0.8520 (t80) REVERT: B 601 CYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8216 (m) REVERT: B 721 ASP cc_start: 0.8436 (p0) cc_final: 0.7785 (t0) outliers start: 54 outliers final: 41 residues processed: 169 average time/residue: 0.2123 time to fit residues: 53.9564 Evaluate side-chains 176 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 126 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 722 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 322 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 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 33 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 32 optimal weight: 0.0970 chunk 144 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.102459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.076583 restraints weight = 29225.819| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.62 r_work: 0.2973 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12428 Z= 0.134 Angle : 0.551 7.364 16864 Z= 0.292 Chirality : 0.041 0.207 1836 Planarity : 0.005 0.069 2098 Dihedral : 7.214 89.545 1660 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.87 % Allowed : 22.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.22), residues: 1436 helix: 2.04 (0.17), residues: 898 sheet: -2.41 (0.52), residues: 76 loop : -1.10 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 389 HIS 0.004 0.001 HIS B 108 PHE 0.027 0.001 PHE B 852 TYR 0.025 0.001 TYR A 306 ARG 0.002 0.000 ARG A 701 Details of bonding type rmsd hydrogen bonds : bond 0.04713 ( 720) hydrogen bonds : angle 4.29123 ( 2130) SS BOND : bond 0.00150 ( 6) SS BOND : angle 0.90653 ( 12) covalent geometry : bond 0.00286 (12422) covalent geometry : angle 0.55089 (16852) ********************** 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 183 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 132 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7078 (pm20) REVERT: A 225 MET cc_start: 0.6841 (tpt) cc_final: 0.5777 (pmm) REVERT: A 243 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8978 (tppp) REVERT: A 255 TYR cc_start: 0.7252 (m-80) cc_final: 0.7024 (m-80) REVERT: A 404 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8433 (mm) REVERT: A 409 ASP cc_start: 0.9096 (OUTLIER) cc_final: 0.8092 (t0) REVERT: A 414 GLN cc_start: 0.8561 (mp10) cc_final: 0.8282 (mp10) REVERT: A 417 GLU cc_start: 0.8975 (tp30) cc_final: 0.8407 (tp30) REVERT: A 534 MET cc_start: 0.7851 (mpt) cc_final: 0.7475 (mpt) REVERT: A 556 PHE cc_start: 0.9241 (t80) cc_final: 0.8941 (t80) REVERT: A 557 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7931 (mm) REVERT: A 661 LYS cc_start: 0.8970 (mtpp) cc_final: 0.8632 (mtpp) REVERT: A 684 SER cc_start: 0.9577 (t) cc_final: 0.9220 (p) REVERT: A 721 ASP cc_start: 0.8352 (p0) cc_final: 0.7775 (t0) REVERT: B 371 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8822 (tt) REVERT: B 555 MET cc_start: 0.8922 (mmm) cc_final: 0.8594 (mmt) REVERT: B 557 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8052 (mm) REVERT: B 569 TYR cc_start: 0.9106 (t80) cc_final: 0.8520 (t80) REVERT: B 601 CYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8216 (m) REVERT: B 721 ASP cc_start: 0.8424 (p0) cc_final: 0.7787 (t0) outliers start: 51 outliers final: 40 residues processed: 170 average time/residue: 0.2173 time to fit residues: 55.7637 Evaluate side-chains 173 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 722 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 322 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 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 4 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 144 optimal weight: 0.0170 chunk 70 optimal weight: 0.8980 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.103024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.077072 restraints weight = 29228.505| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.66 r_work: 0.2986 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12428 Z= 0.127 Angle : 0.546 7.707 16864 Z= 0.287 Chirality : 0.040 0.203 1836 Planarity : 0.005 0.069 2098 Dihedral : 7.170 89.606 1660 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.87 % Allowed : 23.22 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.22), residues: 1436 helix: 2.07 (0.17), residues: 896 sheet: -2.26 (0.52), residues: 66 loop : -1.19 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 389 HIS 0.004 0.001 HIS B 108 PHE 0.026 0.001 PHE B 852 TYR 0.022 0.001 TYR A 306 ARG 0.002 0.000 ARG B 701 Details of bonding type rmsd hydrogen bonds : bond 0.04584 ( 720) hydrogen bonds : angle 4.26104 ( 2130) SS BOND : bond 0.00141 ( 6) SS BOND : angle 0.85948 ( 12) covalent geometry : bond 0.00268 (12422) covalent geometry : angle 0.54534 (16852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5717.83 seconds wall clock time: 101 minutes 11.83 seconds (6071.83 seconds total)