Starting phenix.real_space_refine on Fri Sep 11 16:27:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6g1x_4341/09_2026/6g1x_4341.cif Found real_map, /net/cci-nas-00/data/ceres_data/6g1x_4341/09_2026/6g1x_4341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6g1x_4341/09_2026/6g1x_4341.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6g1x_4341/09_2026/6g1x_4341.cif" model { file = "/net/cci-nas-00/data/ceres_data/6g1x_4341/09_2026/6g1x_4341.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6g1x_4341/09_2026/6g1x_4341.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6g1x_4341/09_2026/6g1x_4341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6g1x_4341/09_2026/6g1x_4341.map" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 30 5.49 5 S 35 5.16 5 C 3572 2.51 5 N 1010 2.21 5 O 1159 1.98 5 H 4182 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9989 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 9349 Classifications: {'peptide': 648} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PTRANS': 20, 'TRANS': 625} Chain breaks: 11 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "X" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 318 Classifications: {'RNAv2': 15} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 8} Link IDs: {'rna3p': 14} Chain: "Y" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 321 Classifications: {'RNAv2': 15} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7932 SG CYS A 907 78.091 28.119 38.244 1.00123.87 S ATOM 7979 SG CYS A 910 81.377 27.168 38.115 1.00130.12 S ATOM 8581 SG CYS A 962 79.713 29.514 41.640 1.00127.98 S Time building chain proxies: 1.78, per 1000 atoms: 0.18 Number of scatterers: 9989 At special positions: 0 Unit cell: (99.51, 83.46, 72.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 35 16.00 P 30 15.00 O 1159 8.00 N 1010 7.00 C 3572 6.00 H 4182 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 131.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 910 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 962 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 907 " 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 7 sheets defined 53.2% alpha, 6.0% beta 13 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 310 through 318 removed outlier: 3.582A pdb=" N GLU A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 322 Processing helix chain 'A' and resid 335 through 355 removed outlier: 4.276A pdb=" N VAL A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 377 removed outlier: 3.919A pdb=" N ALA A 370 " --> pdb=" O LYS A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 400 through 407 removed outlier: 3.546A pdb=" N VAL A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 427 removed outlier: 4.010A pdb=" N LEU A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 445 through 449 Processing helix chain 'A' and resid 457 through 474 removed outlier: 3.593A pdb=" N ARG A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 514 removed outlier: 3.736A pdb=" N ALA A 503 " --> pdb=" O LYS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.768A pdb=" N LEU A 529 " --> pdb=" O ASN A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 567 removed outlier: 3.829A pdb=" N ILE A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 592 removed outlier: 3.699A pdb=" N GLU A 580 " --> pdb=" O THR A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 616 Processing helix chain 'A' and resid 620 through 643 Processing helix chain 'A' and resid 670 through 693 removed outlier: 4.288A pdb=" N ASN A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LYS A 685 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N MET A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 693 " --> pdb=" O LYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 715 removed outlier: 5.022A pdb=" N GLN A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 741 Processing helix chain 'A' and resid 767 through 780 Processing helix chain 'A' and resid 812 through 823 removed outlier: 3.705A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 863 removed outlier: 3.748A pdb=" N GLU A 844 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR A 855 " --> pdb=" O GLU A 851 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A 863 " --> pdb=" O ASN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 895 removed outlier: 3.958A pdb=" N GLN A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 938 Processing helix chain 'A' and resid 1002 through 1006 removed outlier: 3.729A pdb=" N GLU A1005 " --> pdb=" O LYS A1002 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A1006 " --> pdb=" O TRP A1003 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1002 through 1006' Processing sheet with id=AA1, first strand: chain 'A' and resid 328 through 329 removed outlier: 6.403A pdb=" N ILE A 328 " --> pdb=" O THR A 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 360 through 361 removed outlier: 6.140A pdb=" N VAL A 360 " --> pdb=" O ILE A 411 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 440 through 441 Processing sheet with id=AA4, first strand: chain 'A' and resid 751 through 753 removed outlier: 7.107A pdb=" N HIS A 752 " --> pdb=" O ILE A 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 912 through 916 removed outlier: 6.418A pdb=" N LEU A 913 " --> pdb=" O CYS A 907 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N CYS A 907 " --> pdb=" O LEU A 913 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 921 through 923 Processing sheet with id=AA7, first strand: chain 'A' and resid 940 through 942 removed outlier: 6.339A pdb=" N ILE A 960 " --> pdb=" O TRP A 968 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 33 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 1.65 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 4171 1.03 - 1.22: 19 1.22 - 1.42: 2475 1.42 - 1.62: 3415 1.62 - 1.81: 56 Bond restraints: 10136 Sorted by residual: bond pdb=" CG ASN A 897 " pdb=" ND2 ASN A 897 " ideal model delta sigma weight residual 1.328 1.249 0.079 2.10e-02 2.27e+03 1.42e+01 bond pdb=" CB MET A 459 " pdb=" CG MET A 459 " ideal model delta sigma weight residual 1.520 1.433 0.087 3.00e-02 1.11e+03 8.37e+00 bond pdb=" CB THR A 521 " pdb=" CG2 THR A 521 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.64e+00 bond pdb=" CG LEU A 418 " pdb=" CD1 LEU A 418 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.47e+00 bond pdb=" CB ILE A 507 " pdb=" CG2 ILE A 507 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.39e+00 ... (remaining 10131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.53: 17691 10.53 - 21.06: 3 21.06 - 31.59: 0 31.59 - 42.12: 0 42.12 - 52.65: 4 Bond angle restraints: 17698 Sorted by residual: angle pdb=" C ALA A 497 " pdb=" N LYS A 498 " pdb=" H LYS A 498 " ideal model delta sigma weight residual 124.56 71.91 52.65 3.00e+00 1.11e-01 3.08e+02 angle pdb=" C ILE A 399 " pdb=" N SER A 400 " pdb=" H SER A 400 " ideal model delta sigma weight residual 124.71 72.94 51.77 3.00e+00 1.11e-01 2.98e+02 angle pdb=" CA SER A 400 " pdb=" N SER A 400 " pdb=" H SER A 400 " ideal model delta sigma weight residual 114.41 63.13 51.29 3.00e+00 1.11e-01 2.92e+02 angle pdb=" CA LYS A 498 " pdb=" N LYS A 498 " pdb=" H LYS A 498 " ideal model delta sigma weight residual 114.26 65.10 49.16 3.00e+00 1.11e-01 2.68e+02 angle pdb=" C ALA A 497 " pdb=" N LYS A 498 " pdb=" CA LYS A 498 " ideal model delta sigma weight residual 121.18 137.00 -15.82 1.64e+00 3.72e-01 9.30e+01 ... (remaining 17693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.50: 4488 13.50 - 27.00: 373 27.00 - 40.50: 77 40.50 - 54.00: 37 54.00 - 67.51: 13 Dihedral angle restraints: 4988 sinusoidal: 2842 harmonic: 2146 Sorted by residual: dihedral pdb=" CA VAL A 810 " pdb=" C VAL A 810 " pdb=" N THR A 811 " pdb=" CA THR A 811 " ideal model delta harmonic sigma weight residual -180.00 -143.86 -36.14 0 5.00e+00 4.00e-02 5.22e+01 dihedral pdb=" O5' G X 15 " pdb=" C5' G X 15 " pdb=" C4' G X 15 " pdb=" C3' G X 15 " ideal model delta sinusoidal sigma weight residual 60.00 104.58 -44.58 3 6.40e+00 2.44e-02 4.40e+01 dihedral pdb=" CA ILE A 411 " pdb=" C ILE A 411 " pdb=" N ILE A 412 " pdb=" CA ILE A 412 " ideal model delta harmonic sigma weight residual 180.00 150.11 29.89 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 4985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 762 0.065 - 0.131: 140 0.131 - 0.196: 24 0.196 - 0.262: 30 0.262 - 0.327: 1 Chirality restraints: 957 Sorted by residual: chirality pdb=" CB ILE A 361 " pdb=" CA ILE A 361 " pdb=" CG1 ILE A 361 " pdb=" CG2 ILE A 361 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" P A Y 11 " pdb=" OP1 A Y 11 " pdb=" OP2 A Y 11 " pdb=" O5' A Y 11 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" P A Y 15 " pdb=" OP1 A Y 15 " pdb=" OP2 A Y 15 " pdb=" O5' A Y 15 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 954 not shown) Planarity restraints: 1459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 968 " -0.011 2.00e-02 2.50e+03 1.08e-02 4.70e+00 pdb=" CG TRP A 968 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP A 968 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 968 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 968 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 968 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 968 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 968 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 968 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 968 " 0.008 2.00e-02 2.50e+03 pdb=" HD1 TRP A 968 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TRP A 968 " 0.011 2.00e-02 2.50e+03 pdb=" HE3 TRP A 968 " -0.004 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 968 " -0.016 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 968 " 0.003 2.00e-02 2.50e+03 pdb=" HH2 TRP A 968 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 960 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C ILE A 960 " 0.036 2.00e-02 2.50e+03 pdb=" O ILE A 960 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE A 961 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 599 " 0.008 9.50e-02 1.11e+02 1.39e-02 4.15e+00 pdb=" NE ARG A 599 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG A 599 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 599 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 599 " 0.010 2.00e-02 2.50e+03 pdb="HH11 ARG A 599 " 0.011 2.00e-02 2.50e+03 pdb="HH12 ARG A 599 " -0.017 2.00e-02 2.50e+03 pdb="HH21 ARG A 599 " -0.022 2.00e-02 2.50e+03 pdb="HH22 ARG A 599 " 0.023 2.00e-02 2.50e+03 ... (remaining 1456 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 235 2.14 - 2.76: 16986 2.76 - 3.37: 24609 3.37 - 3.99: 31881 3.99 - 4.60: 49905 Nonbonded interactions: 123616 Sorted by model distance: nonbonded pdb=" H LYS A 498 " pdb=" HA LYS A 498 " model vdw 1.530 1.816 nonbonded pdb=" H SER A 400 " pdb=" HA SER A 400 " model vdw 1.640 1.816 nonbonded pdb=" O ILE A 614 " pdb=" H ILE A 618 " model vdw 1.671 2.450 nonbonded pdb=" O THR A 617 " pdb=" HH TYR A 807 " model vdw 1.711 2.450 nonbonded pdb=" HE2 HIS A 927 " pdb=" O2' U X 5 " model vdw 1.720 2.450 ... (remaining 123611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 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: 0.040 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.270 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 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 : 0.014 0.602 5957 Z= 0.573 Angle : 1.021 15.819 8144 Z= 0.547 Chirality : 0.066 0.327 957 Planarity : 0.005 0.046 914 Dihedral : 10.644 67.506 2363 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.66 % Favored : 87.34 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.99 (0.28), residues: 624 helix: -1.39 (0.26), residues: 286 sheet: -4.67 (0.37), residues: 69 loop : -3.47 (0.32), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 820 TYR 0.014 0.003 TYR A 312 PHE 0.020 0.003 PHE A 517 TRP 0.021 0.003 TRP A 968 HIS 0.006 0.002 HIS A 752 Details of bonding type rmsd/Z covalent geometry : bond 0.01176 / 0.51 ( 5954) covalent geometry : angle 1.02057 / 0.55 ( 8144) hydrogen bonds : bond 0.13988 / 9.43 ( 278) hydrogen bonds : angle 6.45720 / 4.53 ( 765) metal coordination : bond 0.35014 / 18.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6235 (mt-10) REVERT: A 568 LYS cc_start: 0.7542 (mmtt) cc_final: 0.7313 (mmmt) REVERT: A 587 GLU cc_start: 0.8525 (tt0) cc_final: 0.8177 (tm-30) REVERT: A 599 ARG cc_start: 0.7606 (ptm-80) cc_final: 0.7177 (ptm160) REVERT: A 615 ASN cc_start: 0.8771 (t0) cc_final: 0.8376 (t0) REVERT: A 674 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8125 (mm-30) REVERT: A 851 GLU cc_start: 0.8489 (tt0) cc_final: 0.8200 (tm-30) REVERT: A 855 TYR cc_start: 0.8519 (m-10) cc_final: 0.8310 (m-10) REVERT: A 923 ILE cc_start: 0.7920 (pp) cc_final: 0.7694 (mt) REVERT: A 981 CYS cc_start: 0.7661 (t) cc_final: 0.7431 (p) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1763 time to fit residues: 38.9080 Evaluate side-chains 107 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 ASN A 509 ASN A 563 GLN A 683 ASN A 711 GLN A 784 ASN ** A 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.148249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.121078 restraints weight = 28979.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.126305 restraints weight = 14029.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.129662 restraints weight = 9017.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.131828 restraints weight = 6751.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.133235 restraints weight = 5555.074| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5957 Z= 0.128 Angle : 0.699 16.371 8144 Z= 0.363 Chirality : 0.043 0.159 957 Planarity : 0.004 0.047 914 Dihedral : 9.718 58.786 1038 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 1.93 % Allowed : 7.36 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.32), residues: 624 helix: 0.38 (0.30), residues: 293 sheet: -4.60 (0.38), residues: 65 loop : -3.02 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 619 TYR 0.016 0.002 TYR A 342 PHE 0.008 0.001 PHE A 551 TRP 0.009 0.001 TRP A 582 HIS 0.010 0.002 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 5954) covalent geometry : angle 0.69922 / 0.36 ( 8144) hydrogen bonds : bond 0.03902 / 2.69 ( 278) hydrogen bonds : angle 4.79139 / 3.37 ( 765) metal coordination : bond 0.00359 / 0.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 LYS cc_start: 0.8614 (mmtp) cc_final: 0.8320 (pttp) REVERT: A 431 ASP cc_start: 0.7037 (p0) cc_final: 0.6797 (p0) REVERT: A 444 ASP cc_start: 0.7231 (t70) cc_final: 0.6530 (t70) REVERT: A 465 GLN cc_start: 0.8305 (tt0) cc_final: 0.8001 (tp40) REVERT: A 515 ASP cc_start: 0.7462 (t0) cc_final: 0.7168 (t0) REVERT: A 568 LYS cc_start: 0.7668 (mmtt) cc_final: 0.7128 (mtpp) REVERT: A 856 LYS cc_start: 0.8554 (mtpt) cc_final: 0.8221 (mtmm) REVERT: A 972 MET cc_start: 0.7694 (ttp) cc_final: 0.7351 (ttp) REVERT: A 981 CYS cc_start: 0.7579 (t) cc_final: 0.7169 (p) outliers start: 11 outliers final: 9 residues processed: 127 average time/residue: 0.1644 time to fit residues: 26.4489 Evaluate side-chains 106 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain A residue 683 ASN Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 915 CYS Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 40.0000 chunk 1 optimal weight: 0.0060 chunk 23 optimal weight: 10.0000 chunk 39 optimal weight: 0.0060 chunk 51 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.1414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 683 ASN ** A 928 HIS ** 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 = 0.3940 r_free = 0.3940 target = 0.145137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.117279 restraints weight = 28847.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.122719 restraints weight = 13494.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.126152 restraints weight = 8498.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.128369 restraints weight = 6313.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129532 restraints weight = 5170.980| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5957 Z= 0.128 Angle : 0.648 16.361 8144 Z= 0.338 Chirality : 0.043 0.146 957 Planarity : 0.003 0.033 914 Dihedral : 9.120 53.554 1038 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.58 % Allowed : 10.33 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.34), residues: 624 helix: 1.18 (0.31), residues: 298 sheet: -4.45 (0.40), residues: 60 loop : -3.00 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 387 TYR 0.015 0.001 TYR A 342 PHE 0.011 0.001 PHE A 517 TRP 0.007 0.001 TRP A 582 HIS 0.005 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 5954) covalent geometry : angle 0.64830 / 0.34 ( 8144) hydrogen bonds : bond 0.03587 / 2.50 ( 278) hydrogen bonds : angle 4.45320 / 3.08 ( 765) metal coordination : bond 0.00071 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 LYS cc_start: 0.8666 (mmtp) cc_final: 0.8103 (pttt) REVERT: A 444 ASP cc_start: 0.7327 (t70) cc_final: 0.6561 (t70) REVERT: A 465 GLN cc_start: 0.8353 (tt0) cc_final: 0.8083 (tp40) REVERT: A 515 ASP cc_start: 0.7748 (t0) cc_final: 0.7378 (t0) REVERT: A 568 LYS cc_start: 0.7620 (mmtt) cc_final: 0.7262 (mtpp) REVERT: A 750 LYS cc_start: 0.7382 (pmmt) cc_final: 0.7137 (tppt) REVERT: A 865 LYS cc_start: 0.8727 (tppt) cc_final: 0.8423 (tptp) outliers start: 9 outliers final: 9 residues processed: 111 average time/residue: 0.1178 time to fit residues: 17.7052 Evaluate side-chains 103 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 683 ASN Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 915 CYS Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 615 ASN A 683 ASN ** A 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.142917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115057 restraints weight = 29167.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.120107 restraints weight = 14242.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.123369 restraints weight = 9244.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.125448 restraints weight = 7012.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.126846 restraints weight = 5842.273| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5957 Z= 0.180 Angle : 0.689 16.239 8144 Z= 0.353 Chirality : 0.045 0.192 957 Planarity : 0.003 0.030 914 Dihedral : 8.951 50.430 1038 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 2.28 % Allowed : 13.13 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.35), residues: 624 helix: 1.48 (0.31), residues: 293 sheet: -4.63 (0.41), residues: 61 loop : -2.82 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 387 TYR 0.014 0.001 TYR A 342 PHE 0.010 0.001 PHE A 401 TRP 0.008 0.001 TRP A 582 HIS 0.005 0.001 HIS A 974 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 ( 5954) covalent geometry : angle 0.68906 / 0.35 ( 8144) hydrogen bonds : bond 0.03586 / 2.49 ( 278) hydrogen bonds : angle 4.43756 / 3.04 ( 765) metal coordination : bond 0.00155 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 LYS cc_start: 0.8629 (mmtp) cc_final: 0.7957 (pttt) REVERT: A 444 ASP cc_start: 0.7385 (t70) cc_final: 0.6694 (t70) REVERT: A 568 LYS cc_start: 0.7789 (mmtt) cc_final: 0.7277 (mttp) REVERT: A 673 ASP cc_start: 0.8582 (t0) cc_final: 0.8335 (t0) REVERT: A 674 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7345 (mm-30) REVERT: A 750 LYS cc_start: 0.7469 (pmmt) cc_final: 0.7145 (tppt) REVERT: A 816 MET cc_start: 0.3750 (tpt) cc_final: 0.3458 (tpt) REVERT: A 865 LYS cc_start: 0.8777 (tppt) cc_final: 0.8495 (tptp) outliers start: 13 outliers final: 13 residues processed: 108 average time/residue: 0.1275 time to fit residues: 18.6689 Evaluate side-chains 110 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 683 ASN Chi-restraints excluded: chain A residue 693 ASN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 915 CYS Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 16 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 41 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.144361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.116215 restraints weight = 28140.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.121493 restraints weight = 13521.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.124824 restraints weight = 8660.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126943 restraints weight = 6500.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.128249 restraints weight = 5375.546| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5957 Z= 0.123 Angle : 0.634 16.351 8144 Z= 0.326 Chirality : 0.043 0.191 957 Planarity : 0.003 0.030 914 Dihedral : 8.679 49.824 1038 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.28 % Allowed : 14.01 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.35), residues: 624 helix: 1.68 (0.31), residues: 301 sheet: -4.41 (0.42), residues: 60 loop : -2.66 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 387 TYR 0.013 0.001 TYR A 342 PHE 0.009 0.001 PHE A 401 TRP 0.007 0.001 TRP A 582 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 5954) covalent geometry : angle 0.63432 / 0.33 ( 8144) hydrogen bonds : bond 0.03436 / 2.42 ( 278) hydrogen bonds : angle 4.26000 / 2.90 ( 765) metal coordination : bond 0.00067 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 LYS cc_start: 0.8597 (mmtp) cc_final: 0.8110 (pttt) REVERT: A 431 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7204 (p0) REVERT: A 444 ASP cc_start: 0.7586 (t70) cc_final: 0.6849 (t70) REVERT: A 509 ASN cc_start: 0.8376 (t0) cc_final: 0.8122 (t0) REVERT: A 568 LYS cc_start: 0.7788 (mmtt) cc_final: 0.7300 (mtpp) REVERT: A 586 MET cc_start: 0.7719 (mmm) cc_final: 0.7170 (mmm) REVERT: A 673 ASP cc_start: 0.8551 (t0) cc_final: 0.8313 (t0) REVERT: A 674 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7364 (mm-30) REVERT: A 688 LYS cc_start: 0.8414 (tptp) cc_final: 0.7887 (tptm) REVERT: A 750 LYS cc_start: 0.7415 (pmmt) cc_final: 0.7052 (tppt) REVERT: A 865 LYS cc_start: 0.8801 (tppt) cc_final: 0.8538 (tptp) REVERT: A 981 CYS cc_start: 0.7867 (t) cc_final: 0.7389 (p) outliers start: 13 outliers final: 10 residues processed: 108 average time/residue: 0.1122 time to fit residues: 16.6505 Evaluate side-chains 107 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 693 ASN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 915 CYS Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 509 ASN A 615 ASN ** A 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.140509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.111615 restraints weight = 28471.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.116892 restraints weight = 13166.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.120259 restraints weight = 8355.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.122372 restraints weight = 6258.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.123753 restraints weight = 5168.148| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5957 Z= 0.210 Angle : 0.733 16.348 8144 Z= 0.369 Chirality : 0.048 0.232 957 Planarity : 0.004 0.037 914 Dihedral : 8.940 48.873 1038 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 21.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 3.50 % Allowed : 14.19 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.35), residues: 624 helix: 1.44 (0.30), residues: 308 sheet: -4.37 (0.44), residues: 61 loop : -2.61 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 599 TYR 0.011 0.001 TYR A 624 PHE 0.016 0.001 PHE A 378 TRP 0.008 0.001 TRP A 582 HIS 0.005 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 ( 5954) covalent geometry : angle 0.73314 / 0.37 ( 8144) hydrogen bonds : bond 0.03793 / 2.68 ( 278) hydrogen bonds : angle 4.51835 / 3.10 ( 765) metal coordination : bond 0.00060 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 LYS cc_start: 0.8635 (mmtp) cc_final: 0.8132 (pttt) REVERT: A 431 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7102 (p0) REVERT: A 444 ASP cc_start: 0.7689 (t70) cc_final: 0.6953 (t70) REVERT: A 502 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6821 (mt-10) REVERT: A 509 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8477 (t0) REVERT: A 586 MET cc_start: 0.7731 (mmm) cc_final: 0.7259 (mmm) REVERT: A 673 ASP cc_start: 0.8548 (t0) cc_final: 0.8341 (t0) REVERT: A 674 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7350 (mm-30) REVERT: A 683 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.8003 (p0) REVERT: A 750 LYS cc_start: 0.7574 (pmmt) cc_final: 0.7018 (tppt) REVERT: A 981 CYS cc_start: 0.7903 (t) cc_final: 0.7523 (p) outliers start: 20 outliers final: 13 residues processed: 108 average time/residue: 0.1111 time to fit residues: 16.8602 Evaluate side-chains 104 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 683 ASN Chi-restraints excluded: chain A residue 693 ASN Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 915 CYS Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.143263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.115017 restraints weight = 28368.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.120179 restraints weight = 13840.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.123417 restraints weight = 8938.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.125437 restraints weight = 6772.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.126655 restraints weight = 5654.671| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5957 Z= 0.118 Angle : 0.642 16.331 8144 Z= 0.326 Chirality : 0.044 0.226 957 Planarity : 0.003 0.031 914 Dihedral : 8.597 49.534 1038 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.10 % Allowed : 16.11 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.36), residues: 624 helix: 1.84 (0.30), residues: 299 sheet: -3.97 (0.51), residues: 55 loop : -2.55 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.011 0.001 TYR A 624 PHE 0.010 0.001 PHE A 551 TRP 0.007 0.001 TRP A 582 HIS 0.005 0.001 HIS A 974 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 5954) covalent geometry : angle 0.64179 / 0.33 ( 8144) hydrogen bonds : bond 0.03406 / 2.42 ( 278) hydrogen bonds : angle 4.27612 / 2.91 ( 765) metal coordination : bond 0.00046 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 LYS cc_start: 0.8580 (mmtp) cc_final: 0.8074 (pttt) REVERT: A 431 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7163 (p0) REVERT: A 444 ASP cc_start: 0.7723 (t70) cc_final: 0.7025 (t70) REVERT: A 488 LEU cc_start: 0.8470 (mp) cc_final: 0.8246 (mp) REVERT: A 673 ASP cc_start: 0.8538 (t0) cc_final: 0.8296 (t0) REVERT: A 674 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7314 (mm-30) REVERT: A 750 LYS cc_start: 0.7406 (pmmt) cc_final: 0.6860 (tppt) REVERT: A 865 LYS cc_start: 0.8779 (tppt) cc_final: 0.8414 (tptp) REVERT: A 981 CYS cc_start: 0.7892 (t) cc_final: 0.7349 (p) outliers start: 12 outliers final: 9 residues processed: 104 average time/residue: 0.1100 time to fit residues: 15.8028 Evaluate side-chains 104 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 693 ASN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 915 CYS Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 28 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 32 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.145154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.117109 restraints weight = 28303.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.122323 restraints weight = 13741.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.125614 restraints weight = 8830.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.127654 restraints weight = 6665.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.129006 restraints weight = 5544.629| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.6156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5957 Z= 0.101 Angle : 0.616 16.368 8144 Z= 0.314 Chirality : 0.043 0.217 957 Planarity : 0.003 0.029 914 Dihedral : 8.412 50.859 1038 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.10 % Allowed : 16.29 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.36), residues: 624 helix: 2.13 (0.31), residues: 299 sheet: -3.81 (0.51), residues: 54 loop : -2.52 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 461 TYR 0.014 0.001 TYR A 624 PHE 0.011 0.001 PHE A 551 TRP 0.007 0.001 TRP A 582 HIS 0.005 0.001 HIS A 974 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 5954) covalent geometry : angle 0.61646 / 0.31 ( 8144) hydrogen bonds : bond 0.03117 / 2.19 ( 278) hydrogen bonds : angle 4.06020 / 2.75 ( 765) metal coordination : bond 0.01085 / 0.54 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 LYS cc_start: 0.8571 (mmtp) cc_final: 0.8098 (pttt) REVERT: A 444 ASP cc_start: 0.7758 (t70) cc_final: 0.6992 (t70) REVERT: A 562 ILE cc_start: 0.8880 (mt) cc_final: 0.8483 (tp) REVERT: A 673 ASP cc_start: 0.8424 (t0) cc_final: 0.8129 (t0) REVERT: A 674 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7340 (mm-30) REVERT: A 750 LYS cc_start: 0.7413 (pmmt) cc_final: 0.6871 (tppt) REVERT: A 865 LYS cc_start: 0.8742 (tppt) cc_final: 0.8464 (tptp) REVERT: A 879 GLN cc_start: 0.8853 (mt0) cc_final: 0.8179 (tp-100) REVERT: A 981 CYS cc_start: 0.7902 (t) cc_final: 0.7406 (p) outliers start: 12 outliers final: 8 residues processed: 110 average time/residue: 0.1222 time to fit residues: 18.4098 Evaluate side-chains 106 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 693 ASN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 915 CYS Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 47 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 0.0870 chunk 37 optimal weight: 3.9990 overall best weight: 1.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.144654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.116732 restraints weight = 28245.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.121879 restraints weight = 13761.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.125071 restraints weight = 8870.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.127100 restraints weight = 6713.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.128475 restraints weight = 5589.509| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5957 Z= 0.113 Angle : 0.622 16.332 8144 Z= 0.315 Chirality : 0.043 0.203 957 Planarity : 0.003 0.027 914 Dihedral : 8.374 50.544 1038 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 1.23 % Allowed : 17.69 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.36), residues: 624 helix: 2.12 (0.30), residues: 306 sheet: -3.82 (0.52), residues: 54 loop : -2.53 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 599 TYR 0.013 0.001 TYR A 624 PHE 0.011 0.001 PHE A 551 TRP 0.007 0.001 TRP A 582 HIS 0.006 0.001 HIS A 974 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 5954) covalent geometry : angle 0.62213 / 0.32 ( 8144) hydrogen bonds : bond 0.03043 / 2.15 ( 278) hydrogen bonds : angle 4.02962 / 2.71 ( 765) metal coordination : bond 0.00098 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 LYS cc_start: 0.8559 (mmtp) cc_final: 0.8093 (pttt) REVERT: A 444 ASP cc_start: 0.7725 (t70) cc_final: 0.6992 (t70) REVERT: A 586 MET cc_start: 0.7811 (mmm) cc_final: 0.7343 (mmm) REVERT: A 673 ASP cc_start: 0.8337 (t0) cc_final: 0.8071 (t0) REVERT: A 674 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7392 (mm-30) REVERT: A 750 LYS cc_start: 0.7417 (pmmt) cc_final: 0.6939 (tppt) REVERT: A 865 LYS cc_start: 0.8721 (tppt) cc_final: 0.8499 (tptp) REVERT: A 879 GLN cc_start: 0.8847 (mt0) cc_final: 0.8180 (tp-100) REVERT: A 981 CYS cc_start: 0.7954 (t) cc_final: 0.7407 (p) outliers start: 7 outliers final: 6 residues processed: 101 average time/residue: 0.1233 time to fit residues: 16.8551 Evaluate side-chains 99 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 693 ASN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.144825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.117186 restraints weight = 27879.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.122436 restraints weight = 13389.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.125639 restraints weight = 8505.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.127728 restraints weight = 6402.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.129061 restraints weight = 5285.725| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.6530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5957 Z= 0.102 Angle : 0.618 16.340 8144 Z= 0.312 Chirality : 0.042 0.186 957 Planarity : 0.003 0.025 914 Dihedral : 8.305 51.322 1038 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.05 % Allowed : 18.04 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.36), residues: 624 helix: 2.43 (0.31), residues: 300 sheet: -3.78 (0.51), residues: 54 loop : -2.46 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 461 TYR 0.013 0.001 TYR A 624 PHE 0.012 0.001 PHE A 551 TRP 0.005 0.001 TRP A 582 HIS 0.006 0.001 HIS A 974 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 5954) covalent geometry : angle 0.61794 / 0.31 ( 8144) hydrogen bonds : bond 0.02963 / 2.09 ( 278) hydrogen bonds : angle 3.94766 / 2.65 ( 765) metal coordination : bond 0.00023 / 0.01 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 LYS cc_start: 0.8563 (mmtp) cc_final: 0.8067 (pttt) REVERT: A 444 ASP cc_start: 0.7738 (t70) cc_final: 0.7000 (t70) REVERT: A 509 ASN cc_start: 0.8480 (t0) cc_final: 0.8243 (t0) REVERT: A 673 ASP cc_start: 0.8324 (t0) cc_final: 0.7986 (t0) REVERT: A 674 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7454 (mm-30) REVERT: A 750 LYS cc_start: 0.7364 (pmmt) cc_final: 0.6884 (tppt) REVERT: A 865 LYS cc_start: 0.8718 (tppt) cc_final: 0.8486 (tptp) REVERT: A 879 GLN cc_start: 0.8810 (mt0) cc_final: 0.8126 (tp-100) REVERT: A 981 CYS cc_start: 0.8006 (t) cc_final: 0.7446 (p) outliers start: 6 outliers final: 6 residues processed: 101 average time/residue: 0.1144 time to fit residues: 15.7366 Evaluate side-chains 102 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 693 ASN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 44 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 469 ASN A 509 ASN A 859 ASN ** A 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.137772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.109480 restraints weight = 28765.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.114147 restraints weight = 14755.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.117094 restraints weight = 9879.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.118962 restraints weight = 7653.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.120047 restraints weight = 6488.978| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.6736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 5957 Z= 0.298 Angle : 0.822 16.152 8144 Z= 0.407 Chirality : 0.053 0.223 957 Planarity : 0.004 0.040 914 Dihedral : 9.232 51.040 1038 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 25.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 1.75 % Allowed : 17.51 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.35), residues: 624 helix: 1.68 (0.30), residues: 305 sheet: -4.22 (0.48), residues: 60 loop : -2.58 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 460 TYR 0.014 0.002 TYR A 381 PHE 0.023 0.002 PHE A 378 TRP 0.008 0.002 TRP A 582 HIS 0.006 0.002 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.30 ( 5954) covalent geometry : angle 0.82170 / 0.41 ( 8144) hydrogen bonds : bond 0.03937 / 2.79 ( 278) hydrogen bonds : angle 4.64101 / 3.16 ( 765) metal coordination : bond 0.00429 / 0.21 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1665.12 seconds wall clock time: 29 minutes 11.05 seconds (1751.05 seconds total)