Starting phenix.real_space_refine on Tue Mar 3 14:02:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n00_24095/03_2026/7n00_24095.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n00_24095/03_2026/7n00_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 { model { file = "/net/cci-nas-00/data/ceres_data/7n00_24095/03_2026/7n00_24095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n00_24095/03_2026/7n00_24095.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n00_24095/03_2026/7n00_24095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n00_24095/03_2026/7n00_24095.map" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 4, 'HIS:plan': 2} 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, 'ASP:plan': 4, 'HIS:plan': 2} 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: 1.43, per 1000 atoms: 0.25 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: 0.45 Conformation dependent library (CDL) restraints added in 329.9 milliseconds 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: 0.17 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: 0.83 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 0.990 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.670 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.380 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (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 ARG 0.002 0.001 ARG C 918 TYR 0.009 0.001 TYR C 826 PHE 0.014 0.002 PHE C 828 TRP 0.010 0.001 TRP C 726 HIS 0.007 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 5953) covalent geometry : angle 0.55420 ( 8056) SS BOND : bond 0.00349 ( 16) SS BOND : angle 0.55538 ( 32) hydrogen bonds : bond 0.18220 ( 188) hydrogen bonds : angle 8.31509 ( 510) *********************** 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 : 0.220 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: 0.7992 (tptp) outliers start: 20 outliers final: 10 residues processed: 244 average time/residue: 0.5086 time to fit residues: 129.9006 Evaluate side-chains 200 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3409 r_free = 0.3409 target = 0.104968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.077318 restraints weight = 10339.237| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.39 r_work: 0.2789 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 5969 Z= 0.172 Angle : 0.591 7.127 8088 Z= 0.310 Chirality : 0.048 0.146 836 Planarity : 0.004 0.047 1077 Dihedral : 5.870 49.853 869 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.79 % Allowed : 19.45 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.27), residues: 798 helix: 0.43 (0.43), residues: 138 sheet: 0.08 (0.32), residues: 188 loop : -0.80 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 806 TYR 0.009 0.001 TYR D 119 PHE 0.018 0.001 PHE D 115 TRP 0.007 0.001 TRP A 726 HIS 0.009 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5953) covalent geometry : angle 0.58881 ( 8056) SS BOND : bond 0.00279 ( 16) SS BOND : angle 1.02946 ( 32) hydrogen bonds : bond 0.04509 ( 188) hydrogen bonds : angle 6.20699 ( 510) *********************** 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 225 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 732 ASP cc_start: 0.8966 (t0) cc_final: 0.8580 (t0) REVERT: A 769 ASP cc_start: 0.8827 (m-30) cc_final: 0.8531 (m-30) REVERT: A 847 ARG cc_start: 0.9188 (mmm-85) cc_final: 0.8935 (mmm-85) REVERT: A 947 ASP cc_start: 0.9110 (t0) cc_final: 0.8683 (t0) REVERT: A 970 LEU cc_start: 0.9452 (mt) cc_final: 0.9079 (mt) REVERT: A 974 GLU cc_start: 0.8403 (pm20) cc_final: 0.8191 (pm20) REVERT: A 994 GLU cc_start: 0.8526 (mp0) cc_final: 0.8270 (mp0) REVERT: C 732 ASP cc_start: 0.8978 (t0) cc_final: 0.8597 (t0) REVERT: C 769 ASP cc_start: 0.8950 (m-30) cc_final: 0.8637 (m-30) REVERT: C 947 ASP cc_start: 0.9169 (t0) cc_final: 0.8805 (t0) REVERT: C 951 ASP cc_start: 0.9075 (m-30) cc_final: 0.8754 (m-30) REVERT: C 970 LEU cc_start: 0.9479 (mt) cc_final: 0.9083 (mt) REVERT: C 994 GLU cc_start: 0.8632 (mp0) cc_final: 0.8229 (mp0) REVERT: B 93 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.7076 (ppp) REVERT: D 100 HIS cc_start: 0.8736 (p-80) cc_final: 0.8483 (p90) REVERT: D 101 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8432 (mp) REVERT: D 133 ARG cc_start: 0.9319 (mtp180) cc_final: 0.9084 (mtp180) outliers start: 22 outliers final: 7 residues processed: 215 average time/residue: 0.5021 time to fit residues: 112.8557 Evaluate side-chains 191 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 182 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 B residue 93 MET Chi-restraints excluded: chain B residue 146 VAL 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 43 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 D 100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.106097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.078674 restraints weight = 10129.135| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.40 r_work: 0.2814 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5969 Z= 0.147 Angle : 0.579 7.530 8088 Z= 0.297 Chirality : 0.047 0.138 836 Planarity : 0.004 0.037 1077 Dihedral : 4.608 32.862 856 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.48 % Allowed : 19.10 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.27), residues: 798 helix: 0.84 (0.46), residues: 138 sheet: 0.13 (0.32), residues: 188 loop : -0.77 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 806 TYR 0.008 0.001 TYR D 119 PHE 0.014 0.001 PHE A 828 TRP 0.005 0.001 TRP A 726 HIS 0.007 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 5953) covalent geometry : angle 0.57797 ( 8056) SS BOND : bond 0.00344 ( 16) SS BOND : angle 0.82647 ( 32) hydrogen bonds : bond 0.04025 ( 188) hydrogen bonds : angle 5.81274 ( 510) *********************** 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 219 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 678 ASP cc_start: 0.9169 (t0) cc_final: 0.8927 (t0) REVERT: A 732 ASP cc_start: 0.9239 (t0) cc_final: 0.8852 (t0) REVERT: A 751 MET cc_start: 0.8014 (mtt) cc_final: 0.7778 (mtt) REVERT: A 769 ASP cc_start: 0.8871 (m-30) cc_final: 0.8491 (m-30) REVERT: A 813 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7966 (tm-30) REVERT: A 947 ASP cc_start: 0.9191 (t0) cc_final: 0.8706 (t0) REVERT: A 951 ASP cc_start: 0.9157 (m-30) cc_final: 0.8859 (m-30) REVERT: A 974 GLU cc_start: 0.8581 (pm20) cc_final: 0.8309 (pm20) REVERT: C 678 ASP cc_start: 0.9199 (t0) cc_final: 0.8947 (t0) REVERT: C 732 ASP cc_start: 0.9262 (t0) cc_final: 0.8860 (t0) REVERT: C 769 ASP cc_start: 0.8972 (m-30) cc_final: 0.8607 (m-30) REVERT: C 804 GLU cc_start: 0.9455 (tp30) cc_final: 0.9171 (tt0) REVERT: C 947 ASP cc_start: 0.9223 (t0) cc_final: 0.8899 (t0) REVERT: C 951 ASP cc_start: 0.8946 (m-30) cc_final: 0.8517 (m-30) REVERT: D 97 PHE cc_start: 0.8278 (t80) cc_final: 0.8021 (t80) REVERT: D 101 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8481 (mp) REVERT: D 133 ARG cc_start: 0.9304 (mtp180) cc_final: 0.9017 (mtp180) outliers start: 26 outliers final: 13 residues processed: 211 average time/residue: 0.4879 time to fit residues: 107.5586 Evaluate side-chains 189 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 805 ILE 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 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 39 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 0.0970 chunk 74 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 overall best weight: 2.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 812 HIS ** A 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.103224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.075680 restraints weight = 10342.731| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.41 r_work: 0.2768 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 5969 Z= 0.250 Angle : 0.622 7.454 8088 Z= 0.321 Chirality : 0.049 0.183 836 Planarity : 0.004 0.038 1077 Dihedral : 4.761 33.577 856 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.10 % Allowed : 22.03 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.28), residues: 798 helix: 0.91 (0.45), residues: 138 sheet: -0.23 (0.31), residues: 204 loop : -0.78 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 806 TYR 0.017 0.001 TYR A 966 PHE 0.014 0.001 PHE C 828 TRP 0.006 0.001 TRP A 726 HIS 0.006 0.001 HIS A 996 Details of bonding type rmsd covalent geometry : bond 0.00538 ( 5953) covalent geometry : angle 0.62132 ( 8056) SS BOND : bond 0.00232 ( 16) SS BOND : angle 0.85889 ( 32) hydrogen bonds : bond 0.04274 ( 188) hydrogen bonds : angle 5.85555 ( 510) *********************** 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 202 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.185 Fit side-chains REVERT: A 678 ASP cc_start: 0.9277 (t0) cc_final: 0.8965 (t0) REVERT: A 732 ASP cc_start: 0.9259 (t0) cc_final: 0.8894 (t0) REVERT: A 748 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8476 (ptpp) REVERT: A 751 MET cc_start: 0.8006 (mtt) cc_final: 0.7802 (mtt) REVERT: A 769 ASP cc_start: 0.8868 (m-30) cc_final: 0.8473 (m-30) REVERT: A 813 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7974 (tm-30) REVERT: A 918 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.7916 (mtp85) REVERT: A 947 ASP cc_start: 0.9226 (t0) cc_final: 0.8715 (t0) REVERT: A 951 ASP cc_start: 0.9212 (m-30) cc_final: 0.8988 (m-30) REVERT: C 678 ASP cc_start: 0.9286 (t0) cc_final: 0.8984 (t0) REVERT: C 732 ASP cc_start: 0.9270 (t0) cc_final: 0.8899 (t0) REVERT: C 751 MET cc_start: 0.7927 (mtt) cc_final: 0.7657 (mtt) REVERT: C 769 ASP cc_start: 0.8967 (m-30) cc_final: 0.8569 (m-30) REVERT: C 946 ASN cc_start: 0.9150 (t0) cc_final: 0.8898 (t0) REVERT: C 947 ASP cc_start: 0.9226 (t0) cc_final: 0.9007 (t0) REVERT: C 951 ASP cc_start: 0.9025 (m-30) cc_final: 0.8717 (m-30) REVERT: D 97 PHE cc_start: 0.8432 (t80) cc_final: 0.7912 (t80) REVERT: D 101 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8486 (mp) REVERT: D 113 LYS cc_start: 0.9539 (tppp) cc_final: 0.9260 (tptp) outliers start: 18 outliers final: 10 residues processed: 197 average time/residue: 0.4851 time to fit residues: 99.9131 Evaluate side-chains 192 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 748 LYS Chi-restraints excluded: chain A residue 855 THR 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 855 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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** 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 = 0.3383 r_free = 0.3383 target = 0.102651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.075127 restraints weight = 10525.433| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.47 r_work: 0.2764 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 5969 Z= 0.245 Angle : 0.632 8.276 8088 Z= 0.326 Chirality : 0.049 0.168 836 Planarity : 0.004 0.035 1077 Dihedral : 4.775 33.879 856 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.10 % Allowed : 23.75 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.28), residues: 798 helix: 1.04 (0.45), residues: 138 sheet: -0.40 (0.31), residues: 222 loop : -0.64 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 806 TYR 0.009 0.001 TYR C 739 PHE 0.012 0.001 PHE C 828 TRP 0.006 0.001 TRP A 726 HIS 0.007 0.001 HIS A 996 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 5953) covalent geometry : angle 0.63085 ( 8056) SS BOND : bond 0.00279 ( 16) SS BOND : angle 0.91070 ( 32) hydrogen bonds : bond 0.04133 ( 188) hydrogen bonds : angle 5.79732 ( 510) *********************** 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 203 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 678 ASP cc_start: 0.9319 (t0) cc_final: 0.9009 (t0) REVERT: A 732 ASP cc_start: 0.9265 (t0) cc_final: 0.8937 (t0) REVERT: A 769 ASP cc_start: 0.8852 (m-30) cc_final: 0.8432 (m-30) REVERT: A 918 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.7870 (mtp85) REVERT: A 947 ASP cc_start: 0.9220 (t0) cc_final: 0.8694 (t0) REVERT: A 951 ASP cc_start: 0.9243 (m-30) cc_final: 0.9026 (m-30) REVERT: A 974 GLU cc_start: 0.8683 (pm20) cc_final: 0.8408 (pm20) REVERT: C 678 ASP cc_start: 0.9335 (t0) cc_final: 0.9023 (t0) REVERT: C 732 ASP cc_start: 0.9264 (t0) cc_final: 0.8930 (t0) REVERT: C 769 ASP cc_start: 0.8939 (m-30) cc_final: 0.8520 (m-30) REVERT: C 804 GLU cc_start: 0.9470 (OUTLIER) cc_final: 0.9005 (tt0) REVERT: C 831 LYS cc_start: 0.9191 (tppp) cc_final: 0.8896 (tptm) REVERT: C 832 ASP cc_start: 0.8970 (p0) cc_final: 0.8667 (p0) REVERT: C 947 ASP cc_start: 0.9233 (t0) cc_final: 0.8865 (t0) REVERT: C 951 ASP cc_start: 0.9062 (m-30) cc_final: 0.8753 (m-30) REVERT: D 97 PHE cc_start: 0.8488 (t80) cc_final: 0.7985 (t80) REVERT: D 101 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8417 (mp) outliers start: 18 outliers final: 11 residues processed: 196 average time/residue: 0.4981 time to fit residues: 102.1455 Evaluate side-chains 188 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 788 GLN Chi-restraints excluded: chain A residue 855 THR 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 788 GLN Chi-restraints excluded: chain C residue 804 GLU Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 913 TRP 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 77 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 GLN A 791 GLN A 812 HIS A 897 GLN C 777 GLN C 791 GLN C 812 HIS ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.105576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.078184 restraints weight = 10356.217| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.46 r_work: 0.2822 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5969 Z= 0.131 Angle : 0.614 9.154 8088 Z= 0.310 Chirality : 0.048 0.169 836 Planarity : 0.004 0.036 1077 Dihedral : 4.604 33.171 856 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.58 % Allowed : 25.13 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.28), residues: 798 helix: 1.27 (0.45), residues: 138 sheet: -0.16 (0.31), residues: 208 loop : -0.68 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 806 TYR 0.012 0.001 TYR A 966 PHE 0.011 0.001 PHE A 828 TRP 0.004 0.001 TRP A 891 HIS 0.006 0.001 HIS A 996 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 5953) covalent geometry : angle 0.61381 ( 8056) SS BOND : bond 0.00187 ( 16) SS BOND : angle 0.61288 ( 32) hydrogen bonds : bond 0.03433 ( 188) hydrogen bonds : angle 5.60657 ( 510) *********************** 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 211 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 678 ASP cc_start: 0.9296 (t0) cc_final: 0.8947 (t0) REVERT: A 732 ASP cc_start: 0.9281 (t0) cc_final: 0.8977 (t0) REVERT: A 769 ASP cc_start: 0.8895 (m-30) cc_final: 0.8468 (m-30) REVERT: A 918 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.7849 (mtp85) REVERT: A 947 ASP cc_start: 0.9229 (t0) cc_final: 0.8713 (t0) REVERT: A 951 ASP cc_start: 0.9183 (m-30) cc_final: 0.8843 (m-30) REVERT: A 970 LEU cc_start: 0.9527 (mt) cc_final: 0.9144 (mp) REVERT: A 974 GLU cc_start: 0.8687 (pm20) cc_final: 0.8413 (pm20) REVERT: C 678 ASP cc_start: 0.9313 (t0) cc_final: 0.8984 (t0) REVERT: C 732 ASP cc_start: 0.9282 (t0) cc_final: 0.8966 (t0) REVERT: C 769 ASP cc_start: 0.8927 (m-30) cc_final: 0.8462 (m-30) REVERT: C 804 GLU cc_start: 0.9455 (tp30) cc_final: 0.9227 (tt0) REVERT: C 946 ASN cc_start: 0.9106 (t0) cc_final: 0.8885 (t0) REVERT: C 947 ASP cc_start: 0.9209 (t0) cc_final: 0.8831 (t0) REVERT: C 950 MET cc_start: 0.9151 (tpp) cc_final: 0.8921 (mpp) REVERT: C 951 ASP cc_start: 0.9005 (m-30) cc_final: 0.8694 (m-30) REVERT: C 970 LEU cc_start: 0.9521 (mt) cc_final: 0.9155 (mp) REVERT: D 97 PHE cc_start: 0.8474 (t80) cc_final: 0.7965 (t80) REVERT: D 101 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8540 (mp) outliers start: 15 outliers final: 7 residues processed: 206 average time/residue: 0.4982 time to fit residues: 107.2741 Evaluate side-chains 190 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 181 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 737 SER Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 913 TRP 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 55 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3397 r_free = 0.3397 target = 0.103607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.076169 restraints weight = 10344.056| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.45 r_work: 0.2789 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5969 Z= 0.209 Angle : 0.669 8.533 8088 Z= 0.340 Chirality : 0.049 0.172 836 Planarity : 0.004 0.041 1077 Dihedral : 4.700 33.964 856 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.24 % Allowed : 26.85 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.28), residues: 798 helix: 1.33 (0.46), residues: 138 sheet: 0.26 (0.33), residues: 188 loop : -0.72 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 806 TYR 0.009 0.001 TYR C 739 PHE 0.012 0.001 PHE A 828 TRP 0.005 0.001 TRP A 814 HIS 0.009 0.001 HIS C 996 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 5953) covalent geometry : angle 0.66911 ( 8056) SS BOND : bond 0.00210 ( 16) SS BOND : angle 0.74889 ( 32) hydrogen bonds : bond 0.03927 ( 188) hydrogen bonds : angle 5.66005 ( 510) *********************** 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 198 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 678 ASP cc_start: 0.9331 (t0) cc_final: 0.9019 (t0) REVERT: A 732 ASP cc_start: 0.9265 (t0) cc_final: 0.8946 (t0) REVERT: A 751 MET cc_start: 0.8889 (pmm) cc_final: 0.8462 (pmm) REVERT: A 769 ASP cc_start: 0.8851 (m-30) cc_final: 0.8431 (m-30) REVERT: A 804 GLU cc_start: 0.9310 (tt0) cc_final: 0.8641 (tt0) REVERT: A 918 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.7901 (mtp85) REVERT: A 947 ASP cc_start: 0.9241 (t0) cc_final: 0.8719 (t0) REVERT: A 951 ASP cc_start: 0.9220 (m-30) cc_final: 0.8986 (m-30) REVERT: A 970 LEU cc_start: 0.9589 (mt) cc_final: 0.9237 (mp) REVERT: C 678 ASP cc_start: 0.9343 (t0) cc_final: 0.9034 (t0) REVERT: C 732 ASP cc_start: 0.9269 (t0) cc_final: 0.8935 (t0) REVERT: C 751 MET cc_start: 0.8835 (pmm) cc_final: 0.8423 (pmm) REVERT: C 769 ASP cc_start: 0.8918 (m-30) cc_final: 0.8451 (m-30) REVERT: C 947 ASP cc_start: 0.9220 (t0) cc_final: 0.8816 (t0) REVERT: C 970 LEU cc_start: 0.9583 (mt) cc_final: 0.9260 (mt) REVERT: C 994 GLU cc_start: 0.8420 (mp0) cc_final: 0.8001 (pm20) REVERT: D 97 PHE cc_start: 0.8423 (t80) cc_final: 0.7898 (t80) REVERT: D 101 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8474 (mp) outliers start: 13 outliers final: 8 residues processed: 195 average time/residue: 0.5110 time to fit residues: 104.1484 Evaluate side-chains 192 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 182 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 911 LYS Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain D residue 101 LEU 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 60 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 24 optimal weight: 0.4980 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.102242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.074762 restraints weight = 10428.414| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.43 r_work: 0.2767 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 5969 Z= 0.259 Angle : 0.715 10.160 8088 Z= 0.364 Chirality : 0.050 0.182 836 Planarity : 0.004 0.040 1077 Dihedral : 4.851 33.889 856 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.41 % Allowed : 27.19 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.28), residues: 798 helix: 1.27 (0.46), residues: 138 sheet: 0.26 (0.33), residues: 188 loop : -0.70 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 806 TYR 0.015 0.001 TYR A 966 PHE 0.012 0.001 PHE C 828 TRP 0.006 0.001 TRP C 726 HIS 0.009 0.001 HIS A 996 Details of bonding type rmsd covalent geometry : bond 0.00562 ( 5953) covalent geometry : angle 0.71509 ( 8056) SS BOND : bond 0.00265 ( 16) SS BOND : angle 0.79987 ( 32) hydrogen bonds : bond 0.04117 ( 188) hydrogen bonds : angle 5.74646 ( 510) *********************** 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 192 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 678 ASP cc_start: 0.9371 (t0) cc_final: 0.9070 (t0) REVERT: A 732 ASP cc_start: 0.9254 (t0) cc_final: 0.8937 (t0) REVERT: A 751 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8540 (pmm) REVERT: A 766 GLU cc_start: 0.9295 (mp0) cc_final: 0.8967 (mp0) REVERT: A 769 ASP cc_start: 0.8867 (m-30) cc_final: 0.8481 (m-30) REVERT: A 918 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.7949 (mtp85) REVERT: A 947 ASP cc_start: 0.9254 (t0) cc_final: 0.8759 (t0) REVERT: A 951 ASP cc_start: 0.9248 (m-30) cc_final: 0.8974 (m-30) REVERT: A 970 LEU cc_start: 0.9578 (mt) cc_final: 0.9285 (mt) REVERT: C 678 ASP cc_start: 0.9356 (t0) cc_final: 0.9051 (t0) REVERT: C 732 ASP cc_start: 0.9242 (t0) cc_final: 0.8907 (t0) REVERT: C 751 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8401 (pmm) REVERT: C 769 ASP cc_start: 0.8930 (m-30) cc_final: 0.8467 (m-30) REVERT: C 947 ASP cc_start: 0.9221 (t0) cc_final: 0.8826 (t0) REVERT: C 970 LEU cc_start: 0.9602 (mt) cc_final: 0.9286 (mt) REVERT: D 97 PHE cc_start: 0.8409 (t80) cc_final: 0.7866 (t80) REVERT: D 101 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8442 (mp) outliers start: 14 outliers final: 8 residues processed: 187 average time/residue: 0.4617 time to fit residues: 90.6789 Evaluate side-chains 182 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 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 751 MET Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 146 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 40 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 74 optimal weight: 0.0020 chunk 47 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.106666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.079074 restraints weight = 10407.840| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.51 r_work: 0.2844 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5969 Z= 0.131 Angle : 0.715 10.254 8088 Z= 0.356 Chirality : 0.049 0.184 836 Planarity : 0.004 0.043 1077 Dihedral : 4.593 33.024 856 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.89 % Allowed : 28.74 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.28), residues: 798 helix: 1.30 (0.46), residues: 138 sheet: -0.01 (0.36), residues: 178 loop : -0.79 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 806 TYR 0.012 0.001 TYR B 131 PHE 0.011 0.001 PHE A 828 TRP 0.004 0.001 TRP C 726 HIS 0.011 0.001 HIS A 989 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 5953) covalent geometry : angle 0.71532 ( 8056) SS BOND : bond 0.00225 ( 16) SS BOND : angle 0.72707 ( 32) hydrogen bonds : bond 0.03290 ( 188) hydrogen bonds : angle 5.54152 ( 510) *********************** 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 209 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 0.215 Fit side-chains REVERT: A 678 ASP cc_start: 0.9315 (t0) cc_final: 0.8986 (t0) REVERT: A 732 ASP cc_start: 0.9262 (t0) cc_final: 0.8997 (t0) REVERT: A 751 MET cc_start: 0.8866 (pmm) cc_final: 0.8530 (pmm) REVERT: A 769 ASP cc_start: 0.8900 (m-30) cc_final: 0.8164 (m-30) REVERT: A 802 GLU cc_start: 0.9152 (mp0) cc_final: 0.8796 (mp0) REVERT: A 804 GLU cc_start: 0.9271 (tt0) cc_final: 0.8558 (tt0) REVERT: A 830 MET cc_start: 0.9380 (mmt) cc_final: 0.9142 (mmm) REVERT: A 918 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.7841 (mtp85) REVERT: A 947 ASP cc_start: 0.9159 (t0) cc_final: 0.8851 (t0) REVERT: A 951 ASP cc_start: 0.9193 (m-30) cc_final: 0.8947 (m-30) REVERT: A 970 LEU cc_start: 0.9522 (mt) cc_final: 0.9206 (mp) REVERT: C 678 ASP cc_start: 0.9331 (t0) cc_final: 0.9005 (t0) REVERT: C 732 ASP cc_start: 0.9260 (t0) cc_final: 0.8945 (t0) REVERT: C 751 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8527 (pmm) REVERT: C 769 ASP cc_start: 0.8951 (m-30) cc_final: 0.8174 (m-30) REVERT: C 803 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8699 (mm-30) REVERT: C 804 GLU cc_start: 0.9445 (tp30) cc_final: 0.9023 (tt0) REVERT: C 970 LEU cc_start: 0.9537 (mt) cc_final: 0.9227 (mp) REVERT: C 994 GLU cc_start: 0.8346 (pm20) cc_final: 0.7980 (pm20) REVERT: B 113 LYS cc_start: 0.9362 (ptpt) cc_final: 0.9085 (mptp) REVERT: B 133 ARG cc_start: 0.9135 (mtp180) cc_final: 0.8777 (mtp180) REVERT: D 97 PHE cc_start: 0.8386 (t80) cc_final: 0.7877 (t80) REVERT: D 101 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8537 (mp) outliers start: 11 outliers final: 7 residues processed: 206 average time/residue: 0.4973 time to fit residues: 107.2394 Evaluate side-chains 198 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 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 751 MET Chi-restraints excluded: chain C residue 913 TRP 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 77 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 0.0670 chunk 68 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.079485 restraints weight = 10347.454| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.43 r_work: 0.2837 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3766 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= 0.141 Angle : 0.759 11.733 8088 Z= 0.376 Chirality : 0.049 0.184 836 Planarity : 0.004 0.047 1077 Dihedral : 4.603 33.709 856 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.89 % Allowed : 29.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.28), residues: 798 helix: 1.33 (0.46), residues: 138 sheet: -0.01 (0.36), residues: 178 loop : -0.82 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 806 TYR 0.016 0.001 TYR A 966 PHE 0.011 0.001 PHE A 828 TRP 0.009 0.001 TRP C 814 HIS 0.010 0.001 HIS A 996 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5953) covalent geometry : angle 0.75927 ( 8056) SS BOND : bond 0.00271 ( 16) SS BOND : angle 0.71279 ( 32) hydrogen bonds : bond 0.03321 ( 188) hydrogen bonds : angle 5.46719 ( 510) ********************** 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 200 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.181 Fit side-chains REVERT: A 678 ASP cc_start: 0.9319 (t0) cc_final: 0.9010 (t0) REVERT: A 732 ASP cc_start: 0.9285 (t0) cc_final: 0.8999 (t0) REVERT: A 751 MET cc_start: 0.8818 (pmm) cc_final: 0.8511 (pmm) REVERT: A 769 ASP cc_start: 0.8893 (m-30) cc_final: 0.8122 (m-30) REVERT: A 802 GLU cc_start: 0.9158 (mp0) cc_final: 0.8794 (mp0) REVERT: A 804 GLU cc_start: 0.9267 (tt0) cc_final: 0.9001 (tt0) REVERT: A 830 MET cc_start: 0.9385 (mmt) cc_final: 0.9132 (mmm) REVERT: A 862 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8047 (tp30) REVERT: A 918 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8517 (mtp-110) REVERT: A 970 LEU cc_start: 0.9543 (mt) cc_final: 0.9257 (mp) REVERT: C 678 ASP cc_start: 0.9331 (t0) cc_final: 0.9016 (t0) REVERT: C 732 ASP cc_start: 0.9257 (t0) cc_final: 0.8956 (t0) REVERT: C 751 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8525 (pmm) REVERT: C 769 ASP cc_start: 0.8935 (m-30) cc_final: 0.8167 (m-30) REVERT: C 803 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8604 (mm-30) REVERT: C 804 GLU cc_start: 0.9446 (tp30) cc_final: 0.9045 (tt0) REVERT: C 970 LEU cc_start: 0.9547 (mt) cc_final: 0.9238 (mp) REVERT: C 994 GLU cc_start: 0.8054 (pm20) cc_final: 0.7838 (pm20) REVERT: B 133 ARG cc_start: 0.9141 (mtp180) cc_final: 0.8776 (mtp180) REVERT: D 101 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8515 (mp) outliers start: 11 outliers final: 7 residues processed: 198 average time/residue: 0.4890 time to fit residues: 101.1813 Evaluate side-chains 194 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 184 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 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 751 MET Chi-restraints excluded: chain C residue 913 TRP 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 22 optimal weight: 6.9990 chunk 55 optimal weight: 0.0040 chunk 1 optimal weight: 0.0770 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.5150 ------------------------------------------------------------------------------- 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 946 ASN C 791 GLN C 812 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 = 0.3462 r_free = 0.3462 target = 0.107914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.080646 restraints weight = 10229.897| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.45 r_work: 0.2870 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5969 Z= 0.133 Angle : 0.764 11.960 8088 Z= 0.376 Chirality : 0.048 0.175 836 Planarity : 0.004 0.046 1077 Dihedral : 4.556 33.777 856 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.89 % Allowed : 29.60 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.28), residues: 798 helix: 1.31 (0.47), residues: 136 sheet: -0.12 (0.35), residues: 174 loop : -0.81 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 806 TYR 0.019 0.001 TYR B 131 PHE 0.011 0.001 PHE A 828 TRP 0.007 0.001 TRP C 814 HIS 0.010 0.001 HIS C 996 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 5953) covalent geometry : angle 0.76441 ( 8056) SS BOND : bond 0.00200 ( 16) SS BOND : angle 0.63827 ( 32) hydrogen bonds : bond 0.03253 ( 188) hydrogen bonds : angle 5.42579 ( 510) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2760.17 seconds wall clock time: 47 minutes 32.23 seconds (2852.23 seconds total)