Starting phenix.real_space_refine on Thu Jul 24 08:42:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n00_24095/07_2025/7n00_24095.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n00_24095/07_2025/7n00_24095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n00_24095/07_2025/7n00_24095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n00_24095/07_2025/7n00_24095.map" model { file = "/net/cci-nas-00/data/ceres_data/7n00_24095/07_2025/7n00_24095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n00_24095/07_2025/7n00_24095.cif" } resolution = 2.27 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 3613 2.51 5 N 1039 2.21 5 O 1113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5817 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2446 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 331} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2450 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 331} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 462 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 459 Classifications: {'peptide': 57} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.42, per 1000 atoms: 0.76 Number of scatterers: 5817 At special positions: 0 Unit cell: (96.642, 93.338, 66.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1113 8.00 N 1039 7.00 C 3613 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 688 " - pdb=" SG CYS A 701 " distance=2.03 Simple disulfide: pdb=" SG CYS A 783 " - pdb=" SG CYS A 794 " distance=2.03 Simple disulfide: pdb=" SG CYS A 906 " - pdb=" SG CYS A 928 " distance=2.03 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS A 995 " distance=2.03 Simple disulfide: pdb=" SG CYS A 990 " - pdb=" SG CYS A1006 " distance=2.03 Simple disulfide: pdb=" SG CYS A1008 " - pdb=" SG CYS A1021 " distance=2.03 Simple disulfide: pdb=" SG CYS C 688 " - pdb=" SG CYS C 701 " distance=2.03 Simple disulfide: pdb=" SG CYS C 783 " - pdb=" SG CYS C 794 " distance=2.03 Simple disulfide: pdb=" SG CYS C 906 " - pdb=" SG CYS C 928 " distance=2.03 Simple disulfide: pdb=" SG CYS C 987 " - pdb=" SG CYS C 995 " distance=2.02 Simple disulfide: pdb=" SG CYS C 990 " - pdb=" SG CYS C1006 " distance=2.03 Simple disulfide: pdb=" SG CYS C1008 " - pdb=" SG CYS C1021 " distance=2.03 Simple disulfide: pdb=" SG CYS B 111 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS D 111 " - pdb=" SG CYS D 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 125 " - pdb=" SG CYS D 134 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 1.3 seconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1338 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 8 sheets defined 22.7% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 697 through 705 Processing helix chain 'A' and resid 787 through 795 Processing helix chain 'A' and resid 799 through 809 Processing helix chain 'A' and resid 895 through 899 Processing helix chain 'A' and resid 906 through 913 Processing helix chain 'C' and resid 697 through 705 Processing helix chain 'C' and resid 717 through 721 removed outlier: 4.241A pdb=" N LEU C 720 " --> pdb=" O GLU C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 795 Processing helix chain 'C' and resid 799 through 809 Processing helix chain 'C' and resid 895 through 899 Processing helix chain 'C' and resid 906 through 914 removed outlier: 3.533A pdb=" N MET C 910 " --> pdb=" O CYS C 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 103 removed outlier: 3.826A pdb=" N LEU B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 121 removed outlier: 3.912A pdb=" N LYS B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 130 through 144 Processing helix chain 'B' and resid 145 through 149 removed outlier: 3.899A pdb=" N GLU B 149 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 103 removed outlier: 3.859A pdb=" N LEU D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 121 Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 130 through 144 Processing sheet with id=AA1, first strand: chain 'A' and resid 682 through 685 removed outlier: 5.374A pdb=" N GLY A 756 " --> pdb=" O VAL A 972 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU A 760 " --> pdb=" O PRO A 968 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE A 762 " --> pdb=" O TYR A 966 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR A 966 " --> pdb=" O ILE A 762 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N ASN A 764 " --> pdb=" O ILE A 964 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N ILE A 964 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 713 through 714 removed outlier: 7.285A pdb=" N MET A 770 " --> pdb=" O MET A 830 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N MET A 830 " --> pdb=" O MET A 770 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR A 825 " --> pdb=" O ILE A 840 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE A 840 " --> pdb=" O THR A 825 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 827 " --> pdb=" O LEU A 838 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 995 through 997 Processing sheet with id=AA4, first strand: chain 'A' and resid 1013 through 1014 Processing sheet with id=AA5, first strand: chain 'C' and resid 682 through 685 removed outlier: 5.386A pdb=" N GLY C 756 " --> pdb=" O VAL C 972 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU C 760 " --> pdb=" O PRO C 968 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE C 762 " --> pdb=" O TYR C 966 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TYR C 966 " --> pdb=" O ILE C 762 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N ASN C 764 " --> pdb=" O ILE C 964 " (cutoff:3.500A) removed outlier: 9.499A pdb=" N ILE C 964 " --> pdb=" O ASN C 764 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 713 through 714 removed outlier: 7.781A pdb=" N MET C 770 " --> pdb=" O MET C 830 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N MET C 830 " --> pdb=" O MET C 770 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR C 825 " --> pdb=" O ILE C 840 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE C 840 " --> pdb=" O THR C 825 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL C 827 " --> pdb=" O LEU C 838 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 995 through 997 Processing sheet with id=AA8, first strand: chain 'C' and resid 1013 through 1014 188 hydrogen bonds defined for protein. 510 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1984 1.34 - 1.46: 1344 1.46 - 1.58: 2553 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 5953 Sorted by residual: bond pdb=" CB VAL C 775 " pdb=" CG1 VAL C 775 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.85e-01 bond pdb=" C GLY C 935 " pdb=" N GLY C 936 " ideal model delta sigma weight residual 1.327 1.319 0.008 9.60e-03 1.09e+04 7.75e-01 bond pdb=" CB PRO C 784 " pdb=" CG PRO C 784 " ideal model delta sigma weight residual 1.506 1.472 0.034 3.90e-02 6.57e+02 7.52e-01 bond pdb=" CB VAL A 775 " pdb=" CG1 VAL A 775 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.45e-01 bond pdb=" C ASP A 947 " pdb=" N PRO A 948 " ideal model delta sigma weight residual 1.335 1.327 0.008 9.40e-03 1.13e+04 7.40e-01 ... (remaining 5948 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 7651 1.10 - 2.19: 331 2.19 - 3.29: 60 3.29 - 4.38: 9 4.38 - 5.48: 5 Bond angle restraints: 8056 Sorted by residual: angle pdb=" N VAL A1019 " pdb=" CA VAL A1019 " pdb=" C VAL A1019 " ideal model delta sigma weight residual 113.71 109.25 4.46 9.50e-01 1.11e+00 2.21e+01 angle pdb=" N LEU B 138 " pdb=" CA LEU B 138 " pdb=" C LEU B 138 " ideal model delta sigma weight residual 111.07 108.43 2.64 1.07e+00 8.73e-01 6.08e+00 angle pdb=" CA VAL A1019 " pdb=" C VAL A1019 " pdb=" N SER A1020 " ideal model delta sigma weight residual 119.87 116.61 3.26 1.34e+00 5.57e-01 5.93e+00 angle pdb=" C HIS C1002 " pdb=" CA HIS C1002 " pdb=" CB HIS C1002 " ideal model delta sigma weight residual 110.42 114.91 -4.49 1.99e+00 2.53e-01 5.09e+00 angle pdb=" C ILE C 805 " pdb=" CA ILE C 805 " pdb=" CB ILE C 805 " ideal model delta sigma weight residual 112.22 109.37 2.85 1.38e+00 5.25e-01 4.27e+00 ... (remaining 8051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 3226 17.27 - 34.55: 172 34.55 - 51.82: 37 51.82 - 69.09: 17 69.09 - 86.37: 6 Dihedral angle restraints: 3458 sinusoidal: 1292 harmonic: 2166 Sorted by residual: dihedral pdb=" CA VAL A 972 " pdb=" C VAL A 972 " pdb=" N MET A 973 " pdb=" CA MET A 973 " ideal model delta harmonic sigma weight residual -180.00 -162.33 -17.67 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA VAL C 972 " pdb=" C VAL C 972 " pdb=" N MET C 973 " pdb=" CA MET C 973 " ideal model delta harmonic sigma weight residual 180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ASP D 124 " pdb=" CB ASP D 124 " pdb=" CG ASP D 124 " pdb=" OD1 ASP D 124 " ideal model delta sinusoidal sigma weight residual -30.00 -88.97 58.97 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 3455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 463 0.028 - 0.057: 200 0.057 - 0.085: 93 0.085 - 0.113: 64 0.113 - 0.141: 16 Chirality restraints: 836 Sorted by residual: chirality pdb=" CA ILE A 839 " pdb=" N ILE A 839 " pdb=" C ILE A 839 " pdb=" CB ILE A 839 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE C 839 " pdb=" N ILE C 839 " pdb=" C ILE C 839 " pdb=" CB ILE C 839 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE A 736 " pdb=" N ILE A 736 " pdb=" C ILE A 736 " pdb=" CB ILE A 736 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 833 not shown) Planarity restraints: 1077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 135 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C ALA D 135 " 0.026 2.00e-02 2.50e+03 pdb=" O ALA D 135 " -0.010 2.00e-02 2.50e+03 pdb=" N ARG D 136 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 137 " 0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C LEU D 137 " -0.026 2.00e-02 2.50e+03 pdb=" O LEU D 137 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU D 138 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 135 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C ALA B 135 " -0.026 2.00e-02 2.50e+03 pdb=" O ALA B 135 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG B 136 " 0.009 2.00e-02 2.50e+03 ... (remaining 1074 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 141 2.69 - 3.24: 5586 3.24 - 3.80: 9695 3.80 - 4.35: 13179 4.35 - 4.90: 21219 Nonbonded interactions: 49820 Sorted by model distance: nonbonded pdb=" OD1 ASN A 864 " pdb=" OG SER A 866 " model vdw 2.138 3.040 nonbonded pdb=" OD1 ASN C 864 " pdb=" OG SER C 866 " model vdw 2.143 3.040 nonbonded pdb=" O MET A 752 " pdb=" NH1 ARG A 847 " model vdw 2.283 3.120 nonbonded pdb=" O PHE D 97 " pdb=" ND1 HIS D 100 " model vdw 2.286 3.120 nonbonded pdb=" OE1 GLU C 803 " pdb=" NH1 ARG C 806 " model vdw 2.313 3.120 ... (remaining 49815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 677 through 985 or (resid 986 and (name N or name CA or na \ me C or name O or name CB )) or resid 987 through 1019 or (resid 1020 and (name \ N or name CA or name C or name O or name CB )) or resid 1021 through 1022)) } ncs_group { reference = (chain 'B' and (resid 93 through 101 or (resid 102 through 103 and (name N or na \ me CA or name C or name O )) or resid 104 through 149)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.240 Find NCS groups from input model: 0.420 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:14.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5969 Z= 0.197 Angle : 0.554 5.479 8088 Z= 0.330 Chirality : 0.046 0.141 836 Planarity : 0.004 0.025 1077 Dihedral : 12.228 86.366 2072 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.44 % Allowed : 5.16 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.26), residues: 798 helix: -0.54 (0.43), residues: 134 sheet: 0.14 (0.36), residues: 128 loop : -0.93 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 726 HIS 0.007 0.001 HIS B 100 PHE 0.014 0.002 PHE C 828 TYR 0.009 0.001 TYR C 826 ARG 0.002 0.001 ARG C 918 Details of bonding type rmsd hydrogen bonds : bond 0.18220 ( 188) hydrogen bonds : angle 8.31509 ( 510) SS BOND : bond 0.00349 ( 16) SS BOND : angle 0.55538 ( 32) covalent geometry : bond 0.00407 ( 5953) covalent geometry : angle 0.55420 ( 8056) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1007 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8439 (p90) REVERT: B 136 ARG cc_start: 0.8061 (mtt90) cc_final: 0.7794 (mtm110) REVERT: D 113 LYS cc_start: 0.8516 (tttp) cc_final: 0.7876 (tptp) outliers start: 20 outliers final: 10 residues processed: 244 average time/residue: 1.1125 time to fit residues: 284.4024 Evaluate side-chains 218 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 207 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain A residue 913 TRP Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain D residue 143 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 GLN A 791 GLN A 812 HIS C 777 GLN C 791 GLN B 120 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.105973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.078685 restraints weight = 10157.883| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.35 r_work: 0.2806 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5969 Z= 0.148 Angle : 0.585 7.411 8088 Z= 0.304 Chirality : 0.047 0.134 836 Planarity : 0.004 0.049 1077 Dihedral : 5.830 50.386 869 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.93 % Allowed : 19.79 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.27), residues: 798 helix: 0.53 (0.44), residues: 138 sheet: 0.06 (0.32), residues: 188 loop : -0.79 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 726 HIS 0.008 0.001 HIS B 100 PHE 0.018 0.001 PHE D 115 TYR 0.009 0.001 TYR D 119 ARG 0.008 0.001 ARG C 806 Details of bonding type rmsd hydrogen bonds : bond 0.04391 ( 188) hydrogen bonds : angle 6.19054 ( 510) SS BOND : bond 0.00222 ( 16) SS BOND : angle 0.95654 ( 32) covalent geometry : bond 0.00315 ( 5953) covalent geometry : angle 0.58323 ( 8056) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 732 ASP cc_start: 0.8930 (t0) cc_final: 0.8522 (t0) REVERT: A 734 TYR cc_start: 0.9448 (m-80) cc_final: 0.9246 (m-80) REVERT: A 769 ASP cc_start: 0.8821 (m-30) cc_final: 0.8522 (m-30) REVERT: A 946 ASN cc_start: 0.8910 (t0) cc_final: 0.8697 (t0) REVERT: A 947 ASP cc_start: 0.9075 (t0) cc_final: 0.8641 (t0) REVERT: A 951 ASP cc_start: 0.9176 (m-30) cc_final: 0.8876 (m-30) REVERT: A 970 LEU cc_start: 0.9433 (mt) cc_final: 0.9056 (mt) REVERT: A 974 GLU cc_start: 0.8411 (pm20) cc_final: 0.8184 (pm20) REVERT: C 732 ASP cc_start: 0.8946 (t0) cc_final: 0.8545 (t0) REVERT: C 734 TYR cc_start: 0.9454 (m-80) cc_final: 0.9253 (m-80) REVERT: C 769 ASP cc_start: 0.8928 (m-30) cc_final: 0.8618 (m-30) REVERT: C 947 ASP cc_start: 0.9129 (t0) cc_final: 0.8780 (t0) REVERT: C 951 ASP cc_start: 0.9041 (m-30) cc_final: 0.8670 (m-30) REVERT: C 970 LEU cc_start: 0.9463 (mt) cc_final: 0.9053 (mt) REVERT: C 994 GLU cc_start: 0.8656 (mp0) cc_final: 0.8258 (mp0) REVERT: D 100 HIS cc_start: 0.8713 (p-80) cc_final: 0.8470 (p90) REVERT: D 101 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8438 (mp) REVERT: D 133 ARG cc_start: 0.9318 (mtp180) cc_final: 0.9115 (mtp180) outliers start: 17 outliers final: 6 residues processed: 225 average time/residue: 1.1709 time to fit residues: 276.4315 Evaluate side-chains 189 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 182 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 913 TRP Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain D residue 101 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 812 HIS D 100 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.104066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.076169 restraints weight = 10271.362| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.42 r_work: 0.2776 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 5969 Z= 0.226 Angle : 0.604 7.696 8088 Z= 0.314 Chirality : 0.048 0.144 836 Planarity : 0.004 0.037 1077 Dihedral : 4.738 33.508 856 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.48 % Allowed : 18.93 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.27), residues: 798 helix: 0.79 (0.45), residues: 138 sheet: -0.43 (0.29), residues: 236 loop : -0.62 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 726 HIS 0.007 0.001 HIS D 100 PHE 0.014 0.001 PHE A 828 TYR 0.009 0.001 TYR A 739 ARG 0.008 0.001 ARG A 806 Details of bonding type rmsd hydrogen bonds : bond 0.04355 ( 188) hydrogen bonds : angle 5.98399 ( 510) SS BOND : bond 0.00245 ( 16) SS BOND : angle 0.91918 ( 32) covalent geometry : bond 0.00485 ( 5953) covalent geometry : angle 0.60252 ( 8056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.726 Fit side-chains REVERT: A 678 ASP cc_start: 0.9208 (t0) cc_final: 0.8968 (t0) REVERT: A 732 ASP cc_start: 0.9248 (t0) cc_final: 0.8853 (t0) REVERT: A 751 MET cc_start: 0.8045 (mtt) cc_final: 0.7777 (mtt) REVERT: A 769 ASP cc_start: 0.8855 (m-30) cc_final: 0.8476 (m-30) REVERT: A 947 ASP cc_start: 0.9215 (t0) cc_final: 0.8738 (t0) REVERT: A 951 ASP cc_start: 0.9194 (m-30) cc_final: 0.8883 (m-30) REVERT: A 974 GLU cc_start: 0.8609 (pm20) cc_final: 0.8401 (pm20) REVERT: A 985 LEU cc_start: 0.9360 (tp) cc_final: 0.9159 (tt) REVERT: C 678 ASP cc_start: 0.9221 (t0) cc_final: 0.8976 (t0) REVERT: C 732 ASP cc_start: 0.9270 (t0) cc_final: 0.8852 (t0) REVERT: C 751 MET cc_start: 0.8055 (mtt) cc_final: 0.7834 (mtt) REVERT: C 769 ASP cc_start: 0.8965 (m-30) cc_final: 0.8613 (m-30) REVERT: C 813 GLU cc_start: 0.8523 (tt0) cc_final: 0.8262 (tm-30) REVERT: C 947 ASP cc_start: 0.9241 (t0) cc_final: 0.8890 (t0) REVERT: C 951 ASP cc_start: 0.9036 (m-30) cc_final: 0.8491 (m-30) REVERT: B 93 MET cc_start: 0.7478 (ppp) cc_final: 0.7223 (ppp) REVERT: D 97 PHE cc_start: 0.8294 (t80) cc_final: 0.7976 (t80) REVERT: D 101 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8468 (mp) REVERT: D 133 ARG cc_start: 0.9314 (mtp180) cc_final: 0.9015 (mtp180) REVERT: D 140 ARG cc_start: 0.8898 (mmm160) cc_final: 0.8661 (mmm160) outliers start: 26 outliers final: 12 residues processed: 203 average time/residue: 1.9039 time to fit residues: 402.7647 Evaluate side-chains 185 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 913 TRP Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 752 MET Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 146 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 69 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 GLN A 791 GLN A 812 HIS C 791 GLN C 812 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.106036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.078288 restraints weight = 10378.136| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.46 r_work: 0.2816 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5969 Z= 0.137 Angle : 0.591 7.491 8088 Z= 0.302 Chirality : 0.047 0.174 836 Planarity : 0.004 0.037 1077 Dihedral : 4.580 32.311 856 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.75 % Allowed : 22.55 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.27), residues: 798 helix: 0.99 (0.45), residues: 138 sheet: 0.18 (0.32), residues: 188 loop : -0.78 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 726 HIS 0.007 0.001 HIS A 996 PHE 0.013 0.001 PHE C 828 TYR 0.010 0.001 TYR C 966 ARG 0.008 0.001 ARG A 806 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 188) hydrogen bonds : angle 5.82361 ( 510) SS BOND : bond 0.00225 ( 16) SS BOND : angle 0.81482 ( 32) covalent geometry : bond 0.00296 ( 5953) covalent geometry : angle 0.58945 ( 8056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 2.051 Fit side-chains revert: symmetry clash REVERT: A 678 ASP cc_start: 0.9237 (t0) cc_final: 0.8894 (t0) REVERT: A 732 ASP cc_start: 0.9277 (t0) cc_final: 0.8970 (t0) REVERT: A 769 ASP cc_start: 0.8881 (m-30) cc_final: 0.8474 (m-30) REVERT: A 918 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.7825 (mtp85) REVERT: A 946 ASN cc_start: 0.9163 (t0) cc_final: 0.8961 (t0) REVERT: A 947 ASP cc_start: 0.9216 (t0) cc_final: 0.8701 (t0) REVERT: A 951 ASP cc_start: 0.9139 (m-30) cc_final: 0.8835 (m-30) REVERT: A 974 GLU cc_start: 0.8650 (pm20) cc_final: 0.8339 (pm20) REVERT: C 678 ASP cc_start: 0.9258 (t0) cc_final: 0.8938 (t0) REVERT: C 732 ASP cc_start: 0.9284 (t0) cc_final: 0.8953 (t0) REVERT: C 769 ASP cc_start: 0.8966 (m-30) cc_final: 0.8567 (m-30) REVERT: C 804 GLU cc_start: 0.9420 (OUTLIER) cc_final: 0.8998 (tt0) REVERT: C 813 GLU cc_start: 0.8525 (tt0) cc_final: 0.8196 (tm-30) REVERT: C 831 LYS cc_start: 0.9029 (tppp) cc_final: 0.8706 (tptm) REVERT: C 947 ASP cc_start: 0.9217 (t0) cc_final: 0.8967 (t0) REVERT: C 951 ASP cc_start: 0.9009 (m-30) cc_final: 0.8556 (m-30) REVERT: B 93 MET cc_start: 0.7496 (ppp) cc_final: 0.7283 (ppp) REVERT: D 97 PHE cc_start: 0.8375 (t80) cc_final: 0.7882 (t80) REVERT: D 101 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8514 (mp) REVERT: D 117 ARG cc_start: 0.9443 (mtt180) cc_final: 0.9233 (mmm-85) REVERT: D 133 ARG cc_start: 0.9301 (mtp180) cc_final: 0.9004 (mtp180) outliers start: 16 outliers final: 10 residues processed: 213 average time/residue: 1.6570 time to fit residues: 372.2604 Evaluate side-chains 200 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 913 TRP Chi-restraints excluded: chain A residue 918 ARG Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 752 MET Chi-restraints excluded: chain C residue 804 GLU Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain D residue 101 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 812 HIS C 812 HIS ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.105898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.078234 restraints weight = 10348.039| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.45 r_work: 0.2822 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5969 Z= 0.142 Angle : 0.602 8.444 8088 Z= 0.306 Chirality : 0.047 0.170 836 Planarity : 0.004 0.035 1077 Dihedral : 4.570 32.559 856 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.10 % Allowed : 24.10 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.27), residues: 798 helix: 1.09 (0.45), residues: 138 sheet: 0.21 (0.32), residues: 188 loop : -0.77 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 891 HIS 0.007 0.001 HIS A 996 PHE 0.026 0.001 PHE D 115 TYR 0.007 0.001 TYR A 739 ARG 0.008 0.001 ARG A 806 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 188) hydrogen bonds : angle 5.72455 ( 510) SS BOND : bond 0.00192 ( 16) SS BOND : angle 0.82174 ( 32) covalent geometry : bond 0.00308 ( 5953) covalent geometry : angle 0.60123 ( 8056) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 0.685 Fit side-chains REVERT: A 678 ASP cc_start: 0.9271 (t0) cc_final: 0.8950 (t0) REVERT: A 732 ASP cc_start: 0.9288 (t0) cc_final: 0.8996 (t0) REVERT: A 769 ASP cc_start: 0.8879 (m-30) cc_final: 0.8466 (m-30) REVERT: A 803 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8959 (mm-30) REVERT: A 852 LYS cc_start: 0.9352 (mtpt) cc_final: 0.9073 (ttmm) REVERT: A 918 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.7891 (mtp85) REVERT: A 947 ASP cc_start: 0.9222 (t0) cc_final: 0.8635 (t0) REVERT: A 950 MET cc_start: 0.9198 (tpp) cc_final: 0.8880 (tpp) REVERT: A 951 ASP cc_start: 0.9135 (m-30) cc_final: 0.8864 (m-30) REVERT: A 974 GLU cc_start: 0.8605 (pm20) cc_final: 0.8345 (pm20) REVERT: C 678 ASP cc_start: 0.9285 (t0) cc_final: 0.8963 (t0) REVERT: C 732 ASP cc_start: 0.9286 (t0) cc_final: 0.8975 (t0) REVERT: C 751 MET cc_start: 0.7875 (mtt) cc_final: 0.7663 (mtt) REVERT: C 769 ASP cc_start: 0.8940 (m-30) cc_final: 0.8514 (m-30) REVERT: C 802 GLU cc_start: 0.9246 (mp0) cc_final: 0.8851 (mp0) REVERT: C 804 GLU cc_start: 0.9429 (OUTLIER) cc_final: 0.9090 (tt0) REVERT: C 813 GLU cc_start: 0.8554 (tt0) cc_final: 0.8268 (tm-30) REVERT: C 831 LYS cc_start: 0.9152 (tppp) cc_final: 0.8919 (tptm) REVERT: C 832 ASP cc_start: 0.8737 (p0) cc_final: 0.8509 (p0) REVERT: C 946 ASN cc_start: 0.9088 (t0) cc_final: 0.8757 (t0) REVERT: C 947 ASP cc_start: 0.9179 (t0) cc_final: 0.8862 (t0) REVERT: C 951 ASP cc_start: 0.8989 (m-30) cc_final: 0.8475 (m-30) REVERT: C 970 LEU cc_start: 0.9522 (mt) cc_final: 0.9133 (mt) REVERT: B 93 MET cc_start: 0.7564 (ppp) cc_final: 0.7313 (ppp) REVERT: D 97 PHE cc_start: 0.8411 (t80) cc_final: 0.7902 (t80) REVERT: D 101 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8529 (mp) REVERT: D 133 ARG cc_start: 0.9292 (mtp180) cc_final: 0.8982 (mtp180) outliers start: 18 outliers final: 10 residues processed: 210 average time/residue: 1.1525 time to fit residues: 253.2080 Evaluate side-chains 200 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 913 TRP Chi-restraints excluded: chain A residue 918 ARG Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 752 MET Chi-restraints excluded: chain C residue 804 GLU Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 146 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 31 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 GLN A 812 HIS C 791 GLN C 812 HIS B 100 HIS ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.105248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.077744 restraints weight = 10248.126| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.44 r_work: 0.2813 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5969 Z= 0.163 Angle : 0.621 9.274 8088 Z= 0.316 Chirality : 0.048 0.172 836 Planarity : 0.004 0.038 1077 Dihedral : 4.568 32.975 856 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.79 % Allowed : 24.96 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.27), residues: 798 helix: 1.24 (0.45), residues: 138 sheet: 0.22 (0.32), residues: 188 loop : -0.76 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 726 HIS 0.008 0.001 HIS A 996 PHE 0.024 0.001 PHE D 115 TYR 0.013 0.001 TYR C 966 ARG 0.009 0.001 ARG A 806 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 188) hydrogen bonds : angle 5.67671 ( 510) SS BOND : bond 0.00212 ( 16) SS BOND : angle 0.77149 ( 32) covalent geometry : bond 0.00354 ( 5953) covalent geometry : angle 0.62020 ( 8056) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 678 ASP cc_start: 0.9293 (t0) cc_final: 0.8970 (t0) REVERT: A 732 ASP cc_start: 0.9277 (t0) cc_final: 0.8986 (t0) REVERT: A 751 MET cc_start: 0.8803 (pmm) cc_final: 0.8591 (pmm) REVERT: A 769 ASP cc_start: 0.8881 (m-30) cc_final: 0.8444 (m-30) REVERT: A 803 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8947 (mm-30) REVERT: A 918 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.7878 (mtp85) REVERT: A 947 ASP cc_start: 0.9217 (t0) cc_final: 0.8688 (t0) REVERT: A 951 ASP cc_start: 0.9140 (m-30) cc_final: 0.8860 (m-30) REVERT: A 974 GLU cc_start: 0.8661 (pm20) cc_final: 0.8385 (pm20) REVERT: C 678 ASP cc_start: 0.9302 (t0) cc_final: 0.8974 (t0) REVERT: C 732 ASP cc_start: 0.9283 (t0) cc_final: 0.9002 (t0) REVERT: C 751 MET cc_start: 0.7885 (mtt) cc_final: 0.7669 (mtt) REVERT: C 769 ASP cc_start: 0.8939 (m-30) cc_final: 0.8484 (m-30) REVERT: C 804 GLU cc_start: 0.9435 (OUTLIER) cc_final: 0.9090 (tt0) REVERT: C 813 GLU cc_start: 0.8589 (tt0) cc_final: 0.8297 (tm-30) REVERT: C 946 ASN cc_start: 0.9123 (t0) cc_final: 0.8797 (t0) REVERT: C 947 ASP cc_start: 0.9207 (t0) cc_final: 0.8926 (t0) REVERT: C 951 ASP cc_start: 0.9025 (m-30) cc_final: 0.8487 (m-30) REVERT: C 970 LEU cc_start: 0.9540 (mt) cc_final: 0.9186 (mt) REVERT: B 93 MET cc_start: 0.7700 (ppp) cc_final: 0.7467 (ppp) REVERT: D 97 PHE cc_start: 0.8440 (t80) cc_final: 0.7940 (t80) REVERT: D 101 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8535 (mp) REVERT: D 117 ARG cc_start: 0.9477 (mtt180) cc_final: 0.9167 (ttm170) REVERT: D 133 ARG cc_start: 0.9302 (mtp180) cc_final: 0.8982 (mtp180) outliers start: 22 outliers final: 9 residues processed: 203 average time/residue: 1.1201 time to fit residues: 238.0966 Evaluate side-chains 198 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 913 TRP Chi-restraints excluded: chain A residue 918 ARG Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 804 GLU Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 146 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 GLN A 812 HIS C 791 GLN C 812 HIS ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.104313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.076447 restraints weight = 10354.076| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.47 r_work: 0.2797 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5969 Z= 0.200 Angle : 0.663 10.422 8088 Z= 0.336 Chirality : 0.049 0.173 836 Planarity : 0.004 0.037 1077 Dihedral : 4.671 33.508 856 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.61 % Allowed : 25.65 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.28), residues: 798 helix: 1.33 (0.45), residues: 138 sheet: 0.22 (0.32), residues: 188 loop : -0.76 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 726 HIS 0.009 0.001 HIS A 996 PHE 0.024 0.001 PHE D 115 TYR 0.008 0.001 TYR C 739 ARG 0.010 0.001 ARG A 806 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 188) hydrogen bonds : angle 5.67266 ( 510) SS BOND : bond 0.00224 ( 16) SS BOND : angle 0.82673 ( 32) covalent geometry : bond 0.00436 ( 5953) covalent geometry : angle 0.66210 ( 8056) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: A 678 ASP cc_start: 0.9324 (t0) cc_final: 0.9017 (t0) REVERT: A 732 ASP cc_start: 0.9278 (t0) cc_final: 0.8959 (t0) REVERT: A 751 MET cc_start: 0.8803 (pmm) cc_final: 0.8449 (pmm) REVERT: A 769 ASP cc_start: 0.8843 (m-30) cc_final: 0.8426 (m-30) REVERT: A 804 GLU cc_start: 0.9299 (tt0) cc_final: 0.9035 (tt0) REVERT: A 918 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.7885 (mtp85) REVERT: A 947 ASP cc_start: 0.9205 (t0) cc_final: 0.8611 (t0) REVERT: A 951 ASP cc_start: 0.9175 (m-30) cc_final: 0.8943 (m-30) REVERT: A 974 GLU cc_start: 0.8666 (pm20) cc_final: 0.8384 (pm20) REVERT: C 678 ASP cc_start: 0.9337 (t0) cc_final: 0.9034 (t0) REVERT: C 732 ASP cc_start: 0.9286 (t0) cc_final: 0.8959 (t0) REVERT: C 751 MET cc_start: 0.7982 (mtt) cc_final: 0.7760 (mtt) REVERT: C 769 ASP cc_start: 0.8926 (m-30) cc_final: 0.8473 (m-30) REVERT: C 804 GLU cc_start: 0.9426 (OUTLIER) cc_final: 0.8925 (tt0) REVERT: C 813 GLU cc_start: 0.8635 (tt0) cc_final: 0.8337 (tm-30) REVERT: C 831 LYS cc_start: 0.9242 (tppp) cc_final: 0.9027 (tppt) REVERT: C 946 ASN cc_start: 0.9155 (t0) cc_final: 0.8921 (t0) REVERT: C 947 ASP cc_start: 0.9225 (t0) cc_final: 0.8872 (t0) REVERT: C 970 LEU cc_start: 0.9569 (mt) cc_final: 0.9248 (mt) REVERT: C 994 GLU cc_start: 0.8301 (pm20) cc_final: 0.7865 (pm20) REVERT: B 93 MET cc_start: 0.7762 (ppp) cc_final: 0.7481 (ppp) REVERT: D 97 PHE cc_start: 0.8449 (t80) cc_final: 0.7909 (t80) REVERT: D 101 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8453 (mp) REVERT: D 117 ARG cc_start: 0.9460 (mtt180) cc_final: 0.9065 (ttm170) outliers start: 21 outliers final: 11 residues processed: 205 average time/residue: 1.1476 time to fit residues: 246.5373 Evaluate side-chains 198 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 913 TRP Chi-restraints excluded: chain A residue 918 ARG Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 804 GLU Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 146 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 76 optimal weight: 0.0370 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 GLN A 812 HIS C 791 GLN C 812 HIS ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.105235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.077777 restraints weight = 10286.935| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.45 r_work: 0.2816 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5969 Z= 0.164 Angle : 0.693 9.897 8088 Z= 0.347 Chirality : 0.049 0.183 836 Planarity : 0.004 0.045 1077 Dihedral : 4.612 33.060 856 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.10 % Allowed : 26.68 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.28), residues: 798 helix: 1.45 (0.45), residues: 138 sheet: 0.26 (0.33), residues: 188 loop : -0.76 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 726 HIS 0.009 0.001 HIS A 996 PHE 0.026 0.001 PHE D 115 TYR 0.015 0.001 TYR A 966 ARG 0.010 0.001 ARG A 806 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 188) hydrogen bonds : angle 5.60445 ( 510) SS BOND : bond 0.00195 ( 16) SS BOND : angle 0.68768 ( 32) covalent geometry : bond 0.00362 ( 5953) covalent geometry : angle 0.69300 ( 8056) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 678 ASP cc_start: 0.9327 (t0) cc_final: 0.9020 (t0) REVERT: A 732 ASP cc_start: 0.9288 (t0) cc_final: 0.8956 (t0) REVERT: A 751 MET cc_start: 0.8790 (pmm) cc_final: 0.8482 (pmm) REVERT: A 769 ASP cc_start: 0.8851 (m-30) cc_final: 0.8429 (m-30) REVERT: A 918 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8534 (mtp-110) REVERT: A 947 ASP cc_start: 0.9236 (t0) cc_final: 0.8765 (t0) REVERT: A 951 ASP cc_start: 0.9172 (m-30) cc_final: 0.8937 (m-30) REVERT: A 974 GLU cc_start: 0.8684 (pm20) cc_final: 0.8390 (pm20) REVERT: C 678 ASP cc_start: 0.9328 (t0) cc_final: 0.9012 (t0) REVERT: C 732 ASP cc_start: 0.9277 (t0) cc_final: 0.8951 (t0) REVERT: C 769 ASP cc_start: 0.8935 (m-30) cc_final: 0.8475 (m-30) REVERT: C 803 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8611 (mm-30) REVERT: C 813 GLU cc_start: 0.8613 (tt0) cc_final: 0.8277 (tm-30) REVERT: C 832 ASP cc_start: 0.9036 (p0) cc_final: 0.8781 (p0) REVERT: C 946 ASN cc_start: 0.9116 (t0) cc_final: 0.8826 (t0) REVERT: C 970 LEU cc_start: 0.9537 (mt) cc_final: 0.9219 (mp) REVERT: C 985 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9030 (tt) REVERT: C 994 GLU cc_start: 0.8114 (pm20) cc_final: 0.7907 (pm20) REVERT: B 93 MET cc_start: 0.7803 (ppp) cc_final: 0.7516 (ppp) REVERT: D 97 PHE cc_start: 0.8389 (t80) cc_final: 0.7831 (t80) REVERT: D 101 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8471 (mp) REVERT: D 117 ARG cc_start: 0.9432 (mtt180) cc_final: 0.9071 (ttm170) REVERT: D 133 ARG cc_start: 0.9316 (mtp180) cc_final: 0.9042 (mtp180) outliers start: 18 outliers final: 9 residues processed: 204 average time/residue: 1.0818 time to fit residues: 231.2307 Evaluate side-chains 199 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 913 TRP Chi-restraints excluded: chain A residue 918 ARG Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain D residue 101 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 8 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 32 optimal weight: 0.1980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 GLN A 812 HIS C 791 GLN C 812 HIS ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.103910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.077056 restraints weight = 10331.747| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.41 r_work: 0.2801 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5969 Z= 0.195 Angle : 0.724 11.627 8088 Z= 0.361 Chirality : 0.049 0.177 836 Planarity : 0.004 0.048 1077 Dihedral : 4.744 33.577 856 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.24 % Allowed : 28.06 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.28), residues: 798 helix: 1.43 (0.45), residues: 138 sheet: 0.28 (0.33), residues: 188 loop : -0.74 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 726 HIS 0.009 0.001 HIS C 996 PHE 0.023 0.001 PHE D 115 TYR 0.014 0.001 TYR B 131 ARG 0.011 0.001 ARG A 806 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 188) hydrogen bonds : angle 5.62266 ( 510) SS BOND : bond 0.00225 ( 16) SS BOND : angle 0.64833 ( 32) covalent geometry : bond 0.00430 ( 5953) covalent geometry : angle 0.72441 ( 8056) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 678 ASP cc_start: 0.9336 (t0) cc_final: 0.9023 (t0) REVERT: A 732 ASP cc_start: 0.9280 (t0) cc_final: 0.8973 (t0) REVERT: A 751 MET cc_start: 0.8825 (pmm) cc_final: 0.8419 (pmm) REVERT: A 769 ASP cc_start: 0.8852 (m-30) cc_final: 0.8459 (m-30) REVERT: A 802 GLU cc_start: 0.9302 (mp0) cc_final: 0.8956 (mp0) REVERT: A 918 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.7882 (mtp85) REVERT: A 947 ASP cc_start: 0.9207 (t0) cc_final: 0.8827 (t0) REVERT: A 951 ASP cc_start: 0.9210 (m-30) cc_final: 0.8930 (m-30) REVERT: A 974 GLU cc_start: 0.8715 (pm20) cc_final: 0.8444 (pm20) REVERT: A 994 GLU cc_start: 0.8475 (mp0) cc_final: 0.8095 (mp0) REVERT: C 678 ASP cc_start: 0.9339 (t0) cc_final: 0.9024 (t0) REVERT: C 732 ASP cc_start: 0.9255 (t0) cc_final: 0.8956 (t0) REVERT: C 751 MET cc_start: 0.8912 (pmm) cc_final: 0.8468 (pmm) REVERT: C 769 ASP cc_start: 0.8920 (m-30) cc_final: 0.8477 (m-30) REVERT: C 804 GLU cc_start: 0.9403 (tp30) cc_final: 0.8991 (tt0) REVERT: C 806 ARG cc_start: 0.9356 (tmm-80) cc_final: 0.9134 (ttp80) REVERT: C 813 GLU cc_start: 0.8613 (tt0) cc_final: 0.8342 (tm-30) REVERT: C 946 ASN cc_start: 0.9088 (t0) cc_final: 0.8795 (t0) REVERT: C 970 LEU cc_start: 0.9560 (mt) cc_final: 0.9269 (mp) REVERT: C 985 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9079 (tt) REVERT: B 93 MET cc_start: 0.7901 (ppp) cc_final: 0.7628 (ppp) REVERT: D 97 PHE cc_start: 0.8366 (t80) cc_final: 0.7801 (t80) REVERT: D 101 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8498 (mp) REVERT: D 140 ARG cc_start: 0.8843 (mmm160) cc_final: 0.8534 (mmm160) outliers start: 13 outliers final: 10 residues processed: 203 average time/residue: 1.2268 time to fit residues: 260.0471 Evaluate side-chains 202 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 913 TRP Chi-restraints excluded: chain A residue 918 ARG Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain D residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.0170 chunk 70 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 812 HIS C 791 GLN C 812 HIS ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.106664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.079528 restraints weight = 10419.104| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.49 r_work: 0.2856 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5969 Z= 0.129 Angle : 0.737 12.059 8088 Z= 0.363 Chirality : 0.048 0.178 836 Planarity : 0.004 0.046 1077 Dihedral : 4.510 33.107 856 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.07 % Allowed : 29.26 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.28), residues: 798 helix: 1.45 (0.45), residues: 138 sheet: -0.07 (0.36), residues: 178 loop : -0.79 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 814 HIS 0.011 0.001 HIS A 989 PHE 0.027 0.001 PHE D 115 TYR 0.016 0.001 TYR C 966 ARG 0.011 0.001 ARG A 806 Details of bonding type rmsd hydrogen bonds : bond 0.03244 ( 188) hydrogen bonds : angle 5.50506 ( 510) SS BOND : bond 0.00178 ( 16) SS BOND : angle 0.60904 ( 32) covalent geometry : bond 0.00296 ( 5953) covalent geometry : angle 0.73721 ( 8056) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 1.090 Fit side-chains REVERT: A 678 ASP cc_start: 0.9320 (t0) cc_final: 0.9004 (t0) REVERT: A 732 ASP cc_start: 0.9272 (t0) cc_final: 0.9002 (t0) REVERT: A 751 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8515 (pmm) REVERT: A 769 ASP cc_start: 0.8877 (m-30) cc_final: 0.8156 (m-30) REVERT: A 802 GLU cc_start: 0.9256 (mp0) cc_final: 0.8894 (mp0) REVERT: A 804 GLU cc_start: 0.9183 (tt0) cc_final: 0.8712 (tt0) REVERT: A 830 MET cc_start: 0.9355 (mmt) cc_final: 0.9146 (mmm) REVERT: A 847 ARG cc_start: 0.9259 (mmm-85) cc_final: 0.9039 (mmm-85) REVERT: A 862 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8054 (tp30) REVERT: A 918 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.7884 (mtp85) REVERT: A 947 ASP cc_start: 0.9108 (t0) cc_final: 0.8857 (t0) REVERT: A 951 ASP cc_start: 0.9143 (m-30) cc_final: 0.8795 (m-30) REVERT: A 974 GLU cc_start: 0.8715 (pm20) cc_final: 0.8471 (pm20) REVERT: A 994 GLU cc_start: 0.8391 (mp0) cc_final: 0.7922 (mp0) REVERT: C 678 ASP cc_start: 0.9320 (t0) cc_final: 0.8998 (t0) REVERT: C 732 ASP cc_start: 0.9278 (t0) cc_final: 0.8947 (t0) REVERT: C 751 MET cc_start: 0.8863 (pmm) cc_final: 0.8518 (pmm) REVERT: C 769 ASP cc_start: 0.8935 (m-30) cc_final: 0.8489 (m-30) REVERT: C 780 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8749 (mt-10) REVERT: C 803 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8544 (mm-30) REVERT: C 804 GLU cc_start: 0.9364 (tp30) cc_final: 0.8960 (tt0) REVERT: C 806 ARG cc_start: 0.9376 (tmm-80) cc_final: 0.9145 (ttp80) REVERT: C 813 GLU cc_start: 0.8599 (tt0) cc_final: 0.8363 (tm-30) REVERT: C 946 ASN cc_start: 0.9044 (t0) cc_final: 0.8619 (t0) REVERT: C 970 LEU cc_start: 0.9517 (mt) cc_final: 0.9218 (mp) REVERT: C 985 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9049 (tt) REVERT: B 93 MET cc_start: 0.7858 (ppp) cc_final: 0.7547 (ppp) REVERT: D 97 PHE cc_start: 0.8369 (t80) cc_final: 0.7838 (t80) REVERT: D 101 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8499 (mp) outliers start: 12 outliers final: 9 residues processed: 207 average time/residue: 1.5140 time to fit residues: 328.4717 Evaluate side-chains 199 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 918 ARG Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain D residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 17 optimal weight: 0.0270 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 GLN A 812 HIS ** A 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 ASN C 791 GLN C 812 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.107180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.080237 restraints weight = 10426.824| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.48 r_work: 0.2862 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5969 Z= 0.135 Angle : 0.772 12.627 8088 Z= 0.378 Chirality : 0.048 0.172 836 Planarity : 0.004 0.047 1077 Dihedral : 4.485 33.290 854 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.89 % Allowed : 30.46 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.28), residues: 798 helix: 1.49 (0.46), residues: 138 sheet: 0.45 (0.38), residues: 158 loop : -0.86 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 814 HIS 0.010 0.001 HIS A 989 PHE 0.026 0.001 PHE D 115 TYR 0.023 0.001 TYR B 131 ARG 0.011 0.001 ARG A 806 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 188) hydrogen bonds : angle 5.48927 ( 510) SS BOND : bond 0.00196 ( 16) SS BOND : angle 0.60584 ( 32) covalent geometry : bond 0.00313 ( 5953) covalent geometry : angle 0.77264 ( 8056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6838.55 seconds wall clock time: 121 minutes 13.86 seconds (7273.86 seconds total)