Starting phenix.real_space_refine on Mon Jul 28 11:44:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6g1x_4341/07_2025/6g1x_4341.cif Found real_map, /net/cci-nas-00/data/ceres_data/6g1x_4341/07_2025/6g1x_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6g1x_4341/07_2025/6g1x_4341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6g1x_4341/07_2025/6g1x_4341.map" model { file = "/net/cci-nas-00/data/ceres_data/6g1x_4341/07_2025/6g1x_4341.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6g1x_4341/07_2025/6g1x_4341.cif" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'GLU:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS: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: {'RNA': 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: {'RNA': 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: 5.61, per 1000 atoms: 0.56 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: 2.63 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 4.36 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: 3.97 Time building geometry restraints manager: 3.32 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 - 14.72: 4629 14.72 - 29.45: 318 29.45 - 44.17: 80 44.17 - 58.89: 42 58.89 - 73.61: 33 Dihedral angle restraints: 5102 sinusoidal: 2956 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=" 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 dihedral pdb=" CA LEU A 938 " pdb=" C LEU A 938 " pdb=" N TYR A 939 " pdb=" CA TYR A 939 " ideal model delta harmonic sigma weight residual 180.00 -150.43 -29.57 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 5099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 787 0.065 - 0.131: 145 0.131 - 0.196: 21 0.196 - 0.262: 3 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=" CG LEU A 508 " pdb=" CB LEU A 508 " pdb=" CD1 LEU A 508 " pdb=" CD2 LEU A 508 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE A 417 " pdb=" CA ILE A 417 " pdb=" CG1 ILE A 417 " pdb=" CG2 ILE A 417 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.96e-01 ... (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: 0.720 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: 0.160 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 35.480 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:3.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 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= 0.574 Angle : 0.989 15.819 8144 Z= 0.545 Chirality : 0.053 0.327 957 Planarity : 0.005 0.046 914 Dihedral : 13.235 73.613 2477 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.96 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.021 0.003 TRP A 968 HIS 0.006 0.002 HIS A 752 PHE 0.020 0.003 PHE A 517 TYR 0.014 0.003 TYR A 312 ARG 0.013 0.002 ARG A 820 Details of bonding type rmsd hydrogen bonds : bond 0.13988 ( 278) hydrogen bonds : angle 6.45720 ( 765) metal coordination : bond 0.35014 ( 3) covalent geometry : bond 0.01173 ( 5954) covalent geometry : angle 0.98887 ( 8144) *********************** 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 : 0.870 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: symmetry clash REVERT: A 504 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6235 (mt-10) REVERT: A 568 LYS cc_start: 0.7542 (mmtt) cc_final: 0.7311 (mmmt) REVERT: A 587 GLU cc_start: 0.8525 (tt0) cc_final: 0.8172 (tm-30) REVERT: A 599 ARG cc_start: 0.7606 (ptm-80) cc_final: 0.7170 (ptm160) REVERT: A 615 ASN cc_start: 0.8771 (t0) cc_final: 0.8377 (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 981 CYS cc_start: 0.7661 (t) cc_final: 0.7397 (p) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.4698 time to fit residues: 102.3587 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 : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN A 509 ASN A 563 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.148937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.121846 restraints weight = 28577.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.127185 restraints weight = 13816.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.130598 restraints weight = 8813.024| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5957 Z= 0.128 Angle : 0.655 16.273 8144 Z= 0.353 Chirality : 0.039 0.157 957 Planarity : 0.004 0.040 914 Dihedral : 15.364 73.900 1152 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.93 % Allowed : 6.83 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.32), residues: 624 helix: 0.36 (0.30), residues: 293 sheet: -4.60 (0.38), residues: 65 loop : -3.05 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 582 HIS 0.010 0.002 HIS A 626 PHE 0.009 0.001 PHE A 551 TYR 0.016 0.002 TYR A 342 ARG 0.004 0.001 ARG A 619 Details of bonding type rmsd hydrogen bonds : bond 0.04029 ( 278) hydrogen bonds : angle 4.79664 ( 765) metal coordination : bond 0.00881 ( 3) covalent geometry : bond 0.00278 ( 5954) covalent geometry : angle 0.65516 ( 8144) *********************** 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 132 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.780 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: A 431 ASP cc_start: 0.7025 (p0) cc_final: 0.6806 (p0) REVERT: A 444 ASP cc_start: 0.7234 (t70) cc_final: 0.6538 (t70) REVERT: A 465 GLN cc_start: 0.8299 (tt0) cc_final: 0.7995 (tp40) REVERT: A 515 ASP cc_start: 0.7523 (t0) cc_final: 0.7224 (t0) REVERT: A 568 LYS cc_start: 0.7672 (mmtt) cc_final: 0.7115 (mtpp) REVERT: A 587 GLU cc_start: 0.8199 (tt0) cc_final: 0.7966 (tm-30) REVERT: A 856 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8237 (mtmm) REVERT: A 974 HIS cc_start: 0.5516 (m-70) cc_final: 0.4856 (m-70) REVERT: A 981 CYS cc_start: 0.7576 (t) cc_final: 0.7130 (p) outliers start: 11 outliers final: 9 residues processed: 126 average time/residue: 0.3981 time to fit residues: 63.0748 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 : 0.828 ------------------------------------------------------------------------------- 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 53 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3964 r_free = 0.3964 target = 0.147488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.120481 restraints weight = 28726.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.125693 restraints weight = 13819.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.129118 restraints weight = 8817.615| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4340 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= 0.107 Angle : 0.593 16.372 8144 Z= 0.322 Chirality : 0.038 0.177 957 Planarity : 0.003 0.032 914 Dihedral : 15.170 73.666 1152 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.75 % Allowed : 9.28 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.35), residues: 624 helix: 1.46 (0.31), residues: 291 sheet: -4.40 (0.41), residues: 60 loop : -2.86 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 582 HIS 0.006 0.001 HIS A 928 PHE 0.012 0.001 PHE A 517 TYR 0.015 0.001 TYR A 342 ARG 0.007 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 278) hydrogen bonds : angle 4.29641 ( 765) metal coordination : bond 0.00131 ( 3) covalent geometry : bond 0.00229 ( 5954) covalent geometry : angle 0.59320 ( 8144) *********************** 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 117 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.733 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: 0.8669 (mmtp) cc_final: 0.8145 (pttt) REVERT: A 444 ASP cc_start: 0.7198 (t70) cc_final: 0.6454 (t70) REVERT: A 515 ASP cc_start: 0.7711 (t0) cc_final: 0.7298 (t0) REVERT: A 568 LYS cc_start: 0.7454 (mmtt) cc_final: 0.7096 (mtpp) REVERT: A 865 LYS cc_start: 0.8700 (tppt) cc_final: 0.8407 (tptp) REVERT: A 972 MET cc_start: 0.7712 (tpp) cc_final: 0.7437 (ttp) outliers start: 10 outliers final: 9 residues processed: 111 average time/residue: 0.3114 time to fit residues: 46.0690 Evaluate side-chains 104 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 19 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.143776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.115591 restraints weight = 28258.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.120645 restraints weight = 13824.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.123863 restraints weight = 9030.302| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5957 Z= 0.161 Angle : 0.613 16.304 8144 Z= 0.332 Chirality : 0.038 0.161 957 Planarity : 0.003 0.029 914 Dihedral : 15.031 74.240 1152 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 2.10 % Allowed : 11.91 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.35), residues: 624 helix: 1.68 (0.31), residues: 293 sheet: -4.57 (0.40), residues: 61 loop : -2.86 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 582 HIS 0.005 0.001 HIS A 974 PHE 0.014 0.001 PHE A 680 TYR 0.013 0.001 TYR A 342 ARG 0.004 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 278) hydrogen bonds : angle 4.32300 ( 765) metal coordination : bond 0.00507 ( 3) covalent geometry : bond 0.00345 ( 5954) covalent geometry : angle 0.61315 ( 8144) *********************** 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 115 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.823 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: 0.8621 (mmtp) cc_final: 0.7936 (pttt) REVERT: A 444 ASP cc_start: 0.7443 (t70) cc_final: 0.6721 (t70) REVERT: A 568 LYS cc_start: 0.7783 (mmtt) cc_final: 0.7300 (mttp) REVERT: A 674 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7443 (mm-30) REVERT: A 700 LYS cc_start: 0.6471 (mppt) cc_final: 0.6144 (mmtt) REVERT: A 750 LYS cc_start: 0.7630 (pmmt) cc_final: 0.7273 (tppt) REVERT: A 912 MET cc_start: 0.8362 (ppp) cc_final: 0.8045 (ppp) REVERT: A 934 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8402 (mp0) outliers start: 12 outliers final: 10 residues processed: 107 average time/residue: 0.3231 time to fit residues: 45.9346 Evaluate side-chains 108 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 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 934 GLU 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 18 optimal weight: 0.9980 chunk 9 optimal weight: 0.1980 chunk 27 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 ASN ** A 974 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 = 0.3934 r_free = 0.3934 target = 0.145251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.117212 restraints weight = 28085.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.122352 restraints weight = 13640.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.125640 restraints weight = 8840.602| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5957 Z= 0.112 Angle : 0.565 16.436 8144 Z= 0.304 Chirality : 0.037 0.153 957 Planarity : 0.003 0.029 914 Dihedral : 14.978 73.947 1152 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.10 % Allowed : 12.78 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.35), residues: 624 helix: 1.95 (0.31), residues: 302 sheet: -4.13 (0.46), residues: 54 loop : -2.80 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 582 HIS 0.004 0.001 HIS A 626 PHE 0.008 0.001 PHE A 681 TYR 0.012 0.001 TYR A 342 ARG 0.003 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03074 ( 278) hydrogen bonds : angle 4.02726 ( 765) metal coordination : bond 0.00379 ( 3) covalent geometry : bond 0.00245 ( 5954) covalent geometry : angle 0.56453 ( 8144) *********************** 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 116 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.725 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: 0.8572 (mmtp) cc_final: 0.7965 (pttt) REVERT: A 431 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7200 (p0) REVERT: A 444 ASP cc_start: 0.7529 (t70) cc_final: 0.6824 (t70) REVERT: A 568 LYS cc_start: 0.7803 (mmtt) cc_final: 0.7287 (mtpp) REVERT: A 673 ASP cc_start: 0.8189 (t0) cc_final: 0.7962 (t0) REVERT: A 674 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7364 (mm-30) REVERT: A 700 LYS cc_start: 0.6441 (mppt) cc_final: 0.6110 (mmtt) REVERT: A 750 LYS cc_start: 0.7620 (pmmt) cc_final: 0.7237 (tppt) REVERT: A 865 LYS cc_start: 0.8815 (tppt) cc_final: 0.8542 (tptp) REVERT: A 912 MET cc_start: 0.8748 (ppp) cc_final: 0.8451 (ppp) REVERT: A 934 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8410 (mp0) outliers start: 12 outliers final: 10 residues processed: 110 average time/residue: 0.3209 time to fit residues: 46.5754 Evaluate side-chains 112 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 934 GLU 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 0 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.144170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115668 restraints weight = 28085.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120835 restraints weight = 13743.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.124010 restraints weight = 8924.116| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5957 Z= 0.120 Angle : 0.574 16.486 8144 Z= 0.308 Chirality : 0.037 0.153 957 Planarity : 0.003 0.029 914 Dihedral : 14.944 74.129 1152 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.45 % Allowed : 13.49 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.36), residues: 624 helix: 2.10 (0.30), residues: 302 sheet: -3.99 (0.47), residues: 54 loop : -2.76 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 582 HIS 0.006 0.001 HIS A 974 PHE 0.011 0.001 PHE A 551 TYR 0.011 0.001 TYR A1018 ARG 0.003 0.000 ARG A 460 Details of bonding type rmsd hydrogen bonds : bond 0.03111 ( 278) hydrogen bonds : angle 3.99611 ( 765) metal coordination : bond 0.00338 ( 3) covalent geometry : bond 0.00257 ( 5954) covalent geometry : angle 0.57369 ( 8144) *********************** 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 115 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.835 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: 0.8554 (mmtp) cc_final: 0.7926 (pttt) REVERT: A 431 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7187 (p0) REVERT: A 444 ASP cc_start: 0.7617 (t70) cc_final: 0.6873 (t70) REVERT: A 568 LYS cc_start: 0.7905 (mmtt) cc_final: 0.7364 (mtpp) REVERT: A 673 ASP cc_start: 0.8357 (t0) cc_final: 0.8149 (t0) REVERT: A 674 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7426 (mm-30) REVERT: A 688 LYS cc_start: 0.8396 (tptp) cc_final: 0.7798 (tptm) REVERT: A 750 LYS cc_start: 0.7541 (pmmt) cc_final: 0.7087 (tppt) REVERT: A 865 LYS cc_start: 0.8828 (tppt) cc_final: 0.8573 (tptp) REVERT: A 981 CYS cc_start: 0.7905 (t) cc_final: 0.7688 (p) outliers start: 14 outliers final: 10 residues processed: 108 average time/residue: 0.3242 time to fit residues: 46.4069 Evaluate side-chains 108 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 617 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 51 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.146340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.119447 restraints weight = 28229.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.124691 restraints weight = 14619.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.126451 restraints weight = 8539.230| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5957 Z= 0.101 Angle : 0.572 16.404 8144 Z= 0.306 Chirality : 0.037 0.187 957 Planarity : 0.003 0.029 914 Dihedral : 14.884 73.901 1152 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.75 % Allowed : 14.89 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.36), residues: 624 helix: 2.31 (0.31), residues: 299 sheet: -3.84 (0.49), residues: 54 loop : -2.67 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 582 HIS 0.005 0.001 HIS A 974 PHE 0.007 0.001 PHE A 551 TYR 0.009 0.001 TYR A 342 ARG 0.002 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 278) hydrogen bonds : angle 3.98652 ( 765) metal coordination : bond 0.00113 ( 3) covalent geometry : bond 0.00221 ( 5954) covalent geometry : angle 0.57203 ( 8144) *********************** 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 109 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.776 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: 0.8571 (mmtp) cc_final: 0.7932 (pttt) REVERT: A 431 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7358 (p0) REVERT: A 444 ASP cc_start: 0.7715 (t70) cc_final: 0.6990 (t70) REVERT: A 628 GLU cc_start: 0.8005 (tt0) cc_final: 0.7799 (tm-30) REVERT: A 673 ASP cc_start: 0.8278 (t0) cc_final: 0.8049 (t0) REVERT: A 674 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7409 (mm-30) REVERT: A 750 LYS cc_start: 0.7571 (pmmt) cc_final: 0.7248 (pttt) REVERT: A 865 LYS cc_start: 0.8775 (tppt) cc_final: 0.8539 (tptp) REVERT: A 879 GLN cc_start: 0.8755 (mt0) cc_final: 0.8103 (tp-100) outliers start: 10 outliers final: 8 residues processed: 104 average time/residue: 0.3457 time to fit residues: 48.0847 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 : 0.813 ------------------------------------------------------------------------------- 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 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 52 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.143230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.114880 restraints weight = 28196.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.119881 restraints weight = 13768.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.123102 restraints weight = 8968.732| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.6101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5957 Z= 0.138 Angle : 0.584 16.287 8144 Z= 0.315 Chirality : 0.037 0.166 957 Planarity : 0.003 0.028 914 Dihedral : 14.848 74.426 1152 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 1.75 % Allowed : 15.24 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.36), residues: 624 helix: 2.22 (0.31), residues: 299 sheet: -3.92 (0.47), residues: 60 loop : -2.61 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 582 HIS 0.005 0.001 HIS A 974 PHE 0.011 0.001 PHE A 378 TYR 0.011 0.001 TYR A1018 ARG 0.002 0.000 ARG A 890 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 278) hydrogen bonds : angle 4.12638 ( 765) metal coordination : bond 0.00727 ( 3) covalent geometry : bond 0.00294 ( 5954) covalent geometry : angle 0.58396 ( 8144) *********************** 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 110 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 1.173 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: A 398 LYS cc_start: 0.8581 (mmtp) cc_final: 0.8088 (pttt) REVERT: A 444 ASP cc_start: 0.7724 (t70) cc_final: 0.6953 (t70) REVERT: A 502 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6870 (mt-10) REVERT: A 673 ASP cc_start: 0.8302 (t0) cc_final: 0.8082 (t0) REVERT: A 674 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7449 (mm-30) REVERT: A 750 LYS cc_start: 0.7562 (pmmt) cc_final: 0.7243 (pttt) REVERT: A 865 LYS cc_start: 0.8833 (tppt) cc_final: 0.8547 (tptp) REVERT: A 929 VAL cc_start: 0.8871 (t) cc_final: 0.8598 (p) outliers start: 10 outliers final: 8 residues processed: 106 average time/residue: 0.3403 time to fit residues: 48.7186 Evaluate side-chains 107 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 725 THR 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 11 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN A 966 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.141833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115120 restraints weight = 28135.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.119589 restraints weight = 14917.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.121560 restraints weight = 9091.203| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.6394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5957 Z= 0.173 Angle : 0.617 16.245 8144 Z= 0.332 Chirality : 0.038 0.169 957 Planarity : 0.003 0.028 914 Dihedral : 14.808 74.579 1152 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 1.58 % Allowed : 16.46 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.36), residues: 624 helix: 1.95 (0.30), residues: 305 sheet: -3.77 (0.49), residues: 62 loop : -2.59 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 582 HIS 0.005 0.001 HIS A 974 PHE 0.014 0.001 PHE A 378 TYR 0.007 0.001 TYR A 342 ARG 0.006 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 278) hydrogen bonds : angle 4.27924 ( 765) metal coordination : bond 0.00158 ( 3) covalent geometry : bond 0.00365 ( 5954) covalent geometry : angle 0.61697 ( 8144) *********************** 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 110 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.769 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: 0.8600 (mmtp) cc_final: 0.8096 (pttt) REVERT: A 403 GLU cc_start: 0.7840 (mp0) cc_final: 0.7582 (mp0) REVERT: A 444 ASP cc_start: 0.7721 (t70) cc_final: 0.6989 (t70) REVERT: A 463 LEU cc_start: 0.9241 (mt) cc_final: 0.9039 (mt) REVERT: A 562 ILE cc_start: 0.8891 (mt) cc_final: 0.8628 (tp) REVERT: A 637 LYS cc_start: 0.8350 (mtmm) cc_final: 0.8119 (mttm) REVERT: A 673 ASP cc_start: 0.8290 (t0) cc_final: 0.8021 (t0) REVERT: A 674 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7450 (mm-30) REVERT: A 750 LYS cc_start: 0.7490 (pmmt) cc_final: 0.7104 (pttt) outliers start: 9 outliers final: 8 residues processed: 106 average time/residue: 0.3297 time to fit residues: 46.3834 Evaluate side-chains 103 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 725 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 0.0000 chunk 52 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.142065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115333 restraints weight = 28473.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.119980 restraints weight = 15357.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.121653 restraints weight = 9408.465| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.6578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5957 Z= 0.162 Angle : 0.616 16.308 8144 Z= 0.330 Chirality : 0.038 0.170 957 Planarity : 0.003 0.027 914 Dihedral : 14.793 74.440 1152 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 23.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 1.23 % Allowed : 16.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.36), residues: 624 helix: 1.89 (0.30), residues: 306 sheet: -3.75 (0.50), residues: 62 loop : -2.54 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 582 HIS 0.005 0.001 HIS A 974 PHE 0.024 0.001 PHE A 378 TYR 0.008 0.001 TYR A 579 ARG 0.003 0.000 ARG A 460 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 278) hydrogen bonds : angle 4.23468 ( 765) metal coordination : bond 0.00115 ( 3) covalent geometry : bond 0.00343 ( 5954) covalent geometry : angle 0.61583 ( 8144) ********************** 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 101 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.830 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: 0.8570 (mmtp) cc_final: 0.8093 (pttt) REVERT: A 403 GLU cc_start: 0.7766 (mp0) cc_final: 0.7479 (mp0) REVERT: A 444 ASP cc_start: 0.7795 (t70) cc_final: 0.7078 (t70) REVERT: A 463 LEU cc_start: 0.9238 (mt) cc_final: 0.9021 (mt) REVERT: A 673 ASP cc_start: 0.8319 (t0) cc_final: 0.8043 (t0) REVERT: A 674 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 750 LYS cc_start: 0.7510 (pmmt) cc_final: 0.7142 (pttt) outliers start: 7 outliers final: 7 residues processed: 98 average time/residue: 0.2983 time to fit residues: 39.7544 Evaluate side-chains 101 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 915 CYS 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 0 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.142001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.115593 restraints weight = 28221.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.119570 restraints weight = 15025.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122180 restraints weight = 9474.789| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.6757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5957 Z= 0.138 Angle : 0.600 16.308 8144 Z= 0.321 Chirality : 0.038 0.169 957 Planarity : 0.003 0.025 914 Dihedral : 14.784 74.336 1152 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 1.40 % Allowed : 17.16 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.36), residues: 624 helix: 1.92 (0.30), residues: 306 sheet: -3.73 (0.50), residues: 62 loop : -2.46 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 582 HIS 0.005 0.001 HIS A 974 PHE 0.017 0.001 PHE A 378 TYR 0.008 0.001 TYR A 579 ARG 0.002 0.000 ARG A 460 Details of bonding type rmsd hydrogen bonds : bond 0.03292 ( 278) hydrogen bonds : angle 4.14915 ( 765) metal coordination : bond 0.00097 ( 3) covalent geometry : bond 0.00294 ( 5954) covalent geometry : angle 0.59976 ( 8144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4226.17 seconds wall clock time: 75 minutes 23.80 seconds (4523.80 seconds total)