Starting phenix.real_space_refine on Thu Mar 14 22:21:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g1x_4341/03_2024/6g1x_4341.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g1x_4341/03_2024/6g1x_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g1x_4341/03_2024/6g1x_4341.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g1x_4341/03_2024/6g1x_4341.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g1x_4341/03_2024/6g1x_4341.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g1x_4341/03_2024/6g1x_4341.pdb" } 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 Residue "A TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.41, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 7.76 Conformation dependent library (CDL) restraints added in 1.1 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: 4.84 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: 3.57 Time building geometry restraints manager: 8.05 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: 63.13 - 77.90: 4 77.90 - 92.67: 0 92.67 - 107.45: 1136 107.45 - 122.22: 14806 122.22 - 137.00: 1752 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 1.850 nonbonded pdb=" O THR A 617 " pdb=" HH TYR A 807 " model vdw 1.711 1.850 nonbonded pdb=" HE2 HIS A 927 " pdb=" O2' U X 5 " model vdw 1.720 1.850 ... (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 ========== 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: 0.480 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: 2.800 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 42.260 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.000 ------------------------------------------------------------------------------- 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 : 0.012 0.115 5954 Z= 0.771 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.869 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: 0.4677 time to fit residues: 101.7629 Evaluate side-chains 107 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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: 0.0670 chunk 50 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN A 513 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5954 Z= 0.167 Angle : 0.632 16.257 8144 Z= 0.341 Chirality : 0.038 0.162 957 Planarity : 0.004 0.040 914 Dihedral : 15.281 73.923 1152 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.10 % Allowed : 7.53 % Favored : 90.37 % 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: -2.35 (0.33), residues: 624 helix: 0.42 (0.30), residues: 296 sheet: -4.66 (0.34), residues: 74 loop : -3.01 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 582 HIS 0.006 0.001 HIS A 626 PHE 0.008 0.001 PHE A 680 TYR 0.016 0.001 TYR A 342 ARG 0.004 0.001 ARG A 806 *********************** 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 136 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 0.803 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: A 398 LYS cc_start: 0.8691 (mmtp) cc_final: 0.8368 (pttt) REVERT: A 465 GLN cc_start: 0.8333 (tt0) cc_final: 0.7908 (tp40) REVERT: A 515 ASP cc_start: 0.7390 (t0) cc_final: 0.7097 (t0) REVERT: A 568 LYS cc_start: 0.7719 (mmtt) cc_final: 0.7310 (mtpp) REVERT: A 587 GLU cc_start: 0.8456 (tt0) cc_final: 0.8153 (tm-30) REVERT: A 599 ARG cc_start: 0.7476 (ptm-80) cc_final: 0.7140 (ptm160) REVERT: A 851 GLU cc_start: 0.8279 (tt0) cc_final: 0.8070 (tm-30) REVERT: A 974 HIS cc_start: 0.5620 (m-70) cc_final: 0.5031 (m-70) outliers start: 12 outliers final: 10 residues processed: 131 average time/residue: 0.3876 time to fit residues: 63.6914 Evaluate side-chains 107 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 566 CYS 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 33 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 ASN A 859 ASN ** A 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5954 Z= 0.212 Angle : 0.620 16.245 8144 Z= 0.335 Chirality : 0.038 0.197 957 Planarity : 0.004 0.044 914 Dihedral : 15.060 74.106 1152 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 2.10 % Allowed : 9.11 % Favored : 88.79 % 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: -1.56 (0.34), residues: 624 helix: 1.34 (0.31), residues: 292 sheet: -4.77 (0.34), residues: 75 loop : -2.73 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 582 HIS 0.006 0.001 HIS A 928 PHE 0.010 0.001 PHE A 517 TYR 0.017 0.002 TYR A 939 ARG 0.007 0.001 ARG A 387 *********************** 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 122 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 0.854 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 398 LYS cc_start: 0.8758 (mmtp) cc_final: 0.8133 (pttp) REVERT: A 444 ASP cc_start: 0.7182 (t70) cc_final: 0.6451 (t70) REVERT: A 465 GLN cc_start: 0.8403 (tt0) cc_final: 0.8150 (tp40) REVERT: A 568 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7399 (mtpp) REVERT: A 587 GLU cc_start: 0.8464 (tt0) cc_final: 0.7950 (tm-30) REVERT: A 599 ARG cc_start: 0.7567 (ptm-80) cc_final: 0.6295 (ptm-80) REVERT: A 624 TYR cc_start: 0.6966 (t80) cc_final: 0.6765 (t80) REVERT: A 674 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7581 (mm-30) REVERT: A 700 LYS cc_start: 0.6427 (mppt) cc_final: 0.6069 (mmtt) REVERT: A 750 LYS cc_start: 0.7484 (pmmt) cc_final: 0.7203 (tppt) REVERT: A 851 GLU cc_start: 0.8479 (tt0) cc_final: 0.8040 (tm-30) REVERT: A 972 MET cc_start: 0.7799 (tpp) cc_final: 0.7564 (ttp) outliers start: 12 outliers final: 12 residues processed: 117 average time/residue: 0.3170 time to fit residues: 48.8534 Evaluate side-chains 113 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 439 SER Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 683 ASN Chi-restraints excluded: chain A residue 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 59 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 ASN ** A 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 5954 Z= 0.336 Angle : 0.684 16.229 8144 Z= 0.371 Chirality : 0.040 0.156 957 Planarity : 0.004 0.031 914 Dihedral : 15.035 74.846 1152 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 26.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 3.68 % Allowed : 12.08 % Favored : 84.24 % 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: -1.75 (0.33), residues: 624 helix: 1.09 (0.29), residues: 294 sheet: -4.57 (0.39), residues: 65 loop : -2.95 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 582 HIS 0.005 0.002 HIS A 928 PHE 0.014 0.002 PHE A 401 TYR 0.012 0.002 TYR A 342 ARG 0.003 0.000 ARG A 460 *********************** 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 126 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 0.912 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: A 398 LYS cc_start: 0.8731 (mmtp) cc_final: 0.8141 (pttp) REVERT: A 444 ASP cc_start: 0.7304 (t70) cc_final: 0.6568 (t70) REVERT: A 465 GLN cc_start: 0.8577 (tt0) cc_final: 0.8321 (tp-100) REVERT: A 509 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8344 (t0) REVERT: A 568 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7444 (mtpp) REVERT: A 587 GLU cc_start: 0.8624 (tt0) cc_final: 0.8040 (tm-30) REVERT: A 599 ARG cc_start: 0.7774 (ptm-80) cc_final: 0.6775 (ptm-80) REVERT: A 674 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7633 (mm-30) REVERT: A 750 LYS cc_start: 0.7598 (pmmt) cc_final: 0.7146 (tppt) REVERT: A 851 GLU cc_start: 0.8537 (tt0) cc_final: 0.8267 (tm-30) REVERT: A 865 LYS cc_start: 0.8877 (tppt) cc_final: 0.8609 (tptp) REVERT: A 934 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8365 (mp0) outliers start: 21 outliers final: 17 residues processed: 115 average time/residue: 0.3134 time to fit residues: 47.7017 Evaluate side-chains 118 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 693 ASN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 915 CYS Chi-restraints excluded: chain A residue 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 36 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 54 optimal weight: 0.0050 chunk 44 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 16 optimal weight: 0.0050 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 overall best weight: 2.6014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 ASN A 509 ASN ** A 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5954 Z= 0.245 Angle : 0.623 16.407 8144 Z= 0.336 Chirality : 0.038 0.155 957 Planarity : 0.003 0.027 914 Dihedral : 14.963 74.393 1152 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 25.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Rotamer: Outliers : 3.33 % Allowed : 14.36 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.49 (0.34), residues: 624 helix: 1.24 (0.29), residues: 304 sheet: -4.42 (0.40), residues: 70 loop : -2.86 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 582 HIS 0.005 0.001 HIS A 928 PHE 0.012 0.001 PHE A 378 TYR 0.012 0.001 TYR A 342 ARG 0.004 0.000 ARG A 599 *********************** 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 120 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 0.771 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: A 398 LYS cc_start: 0.8703 (mmtp) cc_final: 0.8141 (pttt) REVERT: A 444 ASP cc_start: 0.7308 (t70) cc_final: 0.6566 (t70) REVERT: A 587 GLU cc_start: 0.8629 (tt0) cc_final: 0.8116 (tm-30) REVERT: A 599 ARG cc_start: 0.7784 (ptm-80) cc_final: 0.7504 (ptm-80) REVERT: A 674 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7641 (mm-30) REVERT: A 750 LYS cc_start: 0.7628 (pmmt) cc_final: 0.7020 (tppt) REVERT: A 851 GLU cc_start: 0.8662 (tt0) cc_final: 0.8290 (tm-30) REVERT: A 853 MET cc_start: 0.8651 (mmm) cc_final: 0.8388 (tpt) REVERT: A 865 LYS cc_start: 0.8850 (tppt) cc_final: 0.8510 (tptp) REVERT: A 934 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8407 (mp0) outliers start: 19 outliers final: 16 residues processed: 109 average time/residue: 0.3304 time to fit residues: 47.4885 Evaluate side-chains 115 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 409 ASP Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 628 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 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 37 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 0.0470 chunk 53 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.6284 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5954 Z= 0.180 Angle : 0.585 16.395 8144 Z= 0.314 Chirality : 0.037 0.153 957 Planarity : 0.003 0.025 914 Dihedral : 14.897 74.226 1152 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 23.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 2.80 % Allowed : 15.41 % 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: -1.10 (0.35), residues: 624 helix: 1.49 (0.30), residues: 305 sheet: -4.18 (0.47), residues: 61 loop : -2.68 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 582 HIS 0.006 0.001 HIS A 974 PHE 0.009 0.001 PHE A 401 TYR 0.011 0.001 TYR A 342 ARG 0.003 0.000 ARG A 599 *********************** 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 119 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.763 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 398 LYS cc_start: 0.8682 (mmtp) cc_final: 0.8114 (pttt) REVERT: A 444 ASP cc_start: 0.7255 (t70) cc_final: 0.6533 (t70) REVERT: A 587 GLU cc_start: 0.8602 (tt0) cc_final: 0.8095 (tm-30) REVERT: A 599 ARG cc_start: 0.7641 (ptm-80) cc_final: 0.7437 (ptm-80) REVERT: A 673 ASP cc_start: 0.8474 (t0) cc_final: 0.8157 (t0) REVERT: A 674 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7526 (mm-30) REVERT: A 750 LYS cc_start: 0.7556 (pmmt) cc_final: 0.6868 (tppt) REVERT: A 851 GLU cc_start: 0.8629 (tt0) cc_final: 0.8234 (tm-30) REVERT: A 865 LYS cc_start: 0.8879 (tppt) cc_final: 0.8600 (tptp) REVERT: A 912 MET cc_start: 0.8177 (ptt) cc_final: 0.7632 (ppp) REVERT: A 934 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8411 (mp0) outliers start: 16 outliers final: 14 residues processed: 110 average time/residue: 0.2997 time to fit residues: 43.8606 Evaluate side-chains 113 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 457 ASN Chi-restraints excluded: chain A residue 509 ASN 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 628 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 30.0000 chunk 36 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 chunk 39 optimal weight: 0.0050 chunk 38 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.6069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 5954 Z= 0.124 Angle : 0.545 16.609 8144 Z= 0.291 Chirality : 0.037 0.154 957 Planarity : 0.003 0.025 914 Dihedral : 14.839 73.775 1152 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 1.58 % Allowed : 18.04 % Favored : 80.39 % 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: -0.52 (0.36), residues: 624 helix: 2.09 (0.30), residues: 300 sheet: -4.01 (0.49), residues: 61 loop : -2.45 (0.38), residues: 263 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 681 TYR 0.011 0.001 TYR A 342 ARG 0.003 0.000 ARG A 599 *********************** 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 114 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 0.887 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 398 LYS cc_start: 0.8665 (mmtp) cc_final: 0.8099 (pttt) REVERT: A 444 ASP cc_start: 0.7233 (t70) cc_final: 0.6495 (t70) REVERT: A 587 GLU cc_start: 0.8419 (tt0) cc_final: 0.8214 (tm-30) REVERT: A 599 ARG cc_start: 0.7546 (ptm-80) cc_final: 0.7069 (ptm-80) REVERT: A 673 ASP cc_start: 0.8393 (t0) cc_final: 0.8068 (t0) REVERT: A 674 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7532 (mm-30) REVERT: A 750 LYS cc_start: 0.7389 (pmmt) cc_final: 0.6690 (tppt) REVERT: A 851 GLU cc_start: 0.8557 (tt0) cc_final: 0.8123 (tm-30) REVERT: A 865 LYS cc_start: 0.8786 (tppt) cc_final: 0.8533 (tptp) REVERT: A 879 GLN cc_start: 0.8926 (mt0) cc_final: 0.8141 (tp-100) REVERT: A 883 GLU cc_start: 0.6595 (mm-30) cc_final: 0.6245 (mm-30) REVERT: A 912 MET cc_start: 0.8180 (ptt) cc_final: 0.7716 (ppp) outliers start: 9 outliers final: 6 residues processed: 111 average time/residue: 0.3223 time to fit residues: 47.8194 Evaluate side-chains 106 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 693 ASN 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 12 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 43 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN A 509 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.6202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5954 Z= 0.140 Angle : 0.555 16.460 8144 Z= 0.297 Chirality : 0.037 0.185 957 Planarity : 0.003 0.025 914 Dihedral : 14.805 73.944 1152 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.93 % Allowed : 17.69 % Favored : 80.39 % 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: -0.37 (0.36), residues: 624 helix: 2.23 (0.30), residues: 300 sheet: -3.98 (0.47), residues: 65 loop : -2.33 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 582 HIS 0.006 0.001 HIS A 974 PHE 0.009 0.001 PHE A 681 TYR 0.013 0.001 TYR A1018 ARG 0.002 0.000 ARG A 820 *********************** 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 116 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 0.879 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: 0.8630 (mmtp) cc_final: 0.7920 (pttt) REVERT: A 444 ASP cc_start: 0.7228 (t70) cc_final: 0.6513 (t70) REVERT: A 488 LEU cc_start: 0.8518 (mp) cc_final: 0.8317 (mp) REVERT: A 599 ARG cc_start: 0.7409 (ptm-80) cc_final: 0.7010 (ptm-80) REVERT: A 628 GLU cc_start: 0.8176 (tt0) cc_final: 0.7963 (tm-30) REVERT: A 673 ASP cc_start: 0.8369 (t0) cc_final: 0.8086 (t0) REVERT: A 674 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7548 (mm-30) REVERT: A 750 LYS cc_start: 0.7360 (pmmt) cc_final: 0.6646 (tppt) REVERT: A 851 GLU cc_start: 0.8559 (tt0) cc_final: 0.8153 (tm-30) REVERT: A 865 LYS cc_start: 0.8797 (tppt) cc_final: 0.8562 (tptp) REVERT: A 879 GLN cc_start: 0.8900 (mt0) cc_final: 0.8107 (tp-100) REVERT: A 883 GLU cc_start: 0.6653 (mm-30) cc_final: 0.6295 (mm-30) REVERT: A 912 MET cc_start: 0.8189 (ptt) cc_final: 0.7767 (ppp) outliers start: 11 outliers final: 11 residues processed: 109 average time/residue: 0.3167 time to fit residues: 45.6817 Evaluate side-chains 111 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 693 ASN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 915 CYS Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5954 Z= 0.175 Angle : 0.574 16.443 8144 Z= 0.308 Chirality : 0.037 0.180 957 Planarity : 0.003 0.024 914 Dihedral : 14.770 74.168 1152 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 24.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 1.58 % Allowed : 18.74 % Favored : 79.68 % 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: -0.43 (0.36), residues: 624 helix: 2.12 (0.30), residues: 305 sheet: -3.90 (0.46), residues: 76 loop : -2.30 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 582 HIS 0.005 0.001 HIS A 974 PHE 0.014 0.001 PHE A 517 TYR 0.009 0.001 TYR A 342 ARG 0.002 0.000 ARG A 820 *********************** 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 fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 0.817 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: 0.8643 (mmtp) cc_final: 0.7920 (pttt) REVERT: A 444 ASP cc_start: 0.7231 (t70) cc_final: 0.6492 (t70) REVERT: A 628 GLU cc_start: 0.8193 (tt0) cc_final: 0.7993 (tm-30) REVERT: A 673 ASP cc_start: 0.8418 (t0) cc_final: 0.8070 (t0) REVERT: A 674 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7574 (mm-30) REVERT: A 766 MET cc_start: 0.8957 (mmm) cc_final: 0.8717 (mmm) REVERT: A 851 GLU cc_start: 0.8583 (tt0) cc_final: 0.8166 (tm-30) REVERT: A 865 LYS cc_start: 0.8796 (tppt) cc_final: 0.8555 (tptp) REVERT: A 879 GLN cc_start: 0.8974 (mt0) cc_final: 0.8191 (tp-100) REVERT: A 912 MET cc_start: 0.8160 (ptt) cc_final: 0.7731 (ppp) outliers start: 9 outliers final: 8 residues processed: 105 average time/residue: 0.3146 time to fit residues: 43.7204 Evaluate side-chains 107 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 521 THR 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 60 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 41 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.6510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5954 Z= 0.182 Angle : 0.580 16.410 8144 Z= 0.310 Chirality : 0.037 0.171 957 Planarity : 0.003 0.023 914 Dihedral : 14.737 74.375 1152 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 25.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 1.75 % Allowed : 18.74 % Favored : 79.51 % 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: -0.38 (0.36), residues: 624 helix: 2.15 (0.30), residues: 305 sheet: -3.79 (0.54), residues: 67 loop : -2.38 (0.39), residues: 252 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 0.013 0.001 TYR A1018 ARG 0.003 0.000 ARG A 599 ********************** 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 106 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 0.860 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: 0.8626 (mmtp) cc_final: 0.7945 (pttt) REVERT: A 444 ASP cc_start: 0.7319 (t70) cc_final: 0.6567 (t70) REVERT: A 673 ASP cc_start: 0.8463 (t0) cc_final: 0.8093 (t0) REVERT: A 674 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 851 GLU cc_start: 0.8604 (tt0) cc_final: 0.8207 (tm-30) REVERT: A 912 MET cc_start: 0.8109 (ptt) cc_final: 0.7699 (ppp) outliers start: 10 outliers final: 10 residues processed: 101 average time/residue: 0.3017 time to fit residues: 41.0275 Evaluate side-chains 105 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 521 THR 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 52 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 46 optimal weight: 8.9990 chunk 2 optimal weight: 0.0770 chunk 37 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 overall best weight: 1.9144 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.141916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.115665 restraints weight = 28827.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.119657 restraints weight = 15381.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.122104 restraints weight = 9742.156| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.6685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5954 Z= 0.196 Angle : 0.590 16.401 8144 Z= 0.316 Chirality : 0.037 0.169 957 Planarity : 0.003 0.024 914 Dihedral : 14.740 74.357 1152 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 26.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 1.75 % Allowed : 19.09 % Favored : 79.16 % 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: -0.34 (0.36), residues: 624 helix: 2.19 (0.30), residues: 305 sheet: -3.87 (0.54), residues: 65 loop : -2.37 (0.39), residues: 254 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 0.013 0.001 PHE A 378 TYR 0.012 0.001 TYR A1018 ARG 0.003 0.000 ARG A 461 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2622.09 seconds wall clock time: 47 minutes 4.59 seconds (2824.59 seconds total)