Starting phenix.real_space_refine on Tue Jun 17 14:17:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xcr_33126/06_2025/7xcr_33126.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xcr_33126/06_2025/7xcr_33126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xcr_33126/06_2025/7xcr_33126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xcr_33126/06_2025/7xcr_33126.map" model { file = "/net/cci-nas-00/data/ceres_data/7xcr_33126/06_2025/7xcr_33126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xcr_33126/06_2025/7xcr_33126.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5986 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 26 5.16 5 C 8789 2.51 5 N 2847 2.21 5 O 3446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15400 Number of models: 1 Model: "" Number of chains: 13 Chain: "L" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "F" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "K" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2671 Classifications: {'peptide': 328} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 308} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 residue: pdb=" N ARG L 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG L 74 " occ=0.45 residue: pdb=" N GLY L 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY L 75 " occ=0.25 residue: pdb=" N GLY L 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY L 76 " occ=0.25 Time building chain proxies: 8.90, per 1000 atoms: 0.58 Number of scatterers: 15400 At special positions: 0 Unit cell: (120.96, 122.04, 130.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 292 15.00 O 3446 8.00 N 2847 7.00 C 8789 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 1.3 seconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2206 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 55.7% alpha, 5.5% beta 135 base pairs and 277 stacking pairs defined. Time for finding SS restraints: 7.26 Creating SS restraints... Processing helix chain 'L' and resid 22 through 34 removed outlier: 4.048A pdb=" N GLN L 31 " --> pdb=" O LYS L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 41 removed outlier: 4.040A pdb=" N GLN L 41 " --> pdb=" O PRO L 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 35 Processing helix chain 'F' and resid 49 through 57 removed outlier: 3.598A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.524A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.699A pdb=" N LYS H 46 " --> pdb=" O TYR H 42 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.616A pdb=" N ILE H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.501A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 46 removed outlier: 4.028A pdb=" N ARG K 42 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP K 43 " --> pdb=" O GLU K 39 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU K 46 " --> pdb=" O ARG K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 55 Processing helix chain 'K' and resid 67 through 81 removed outlier: 4.338A pdb=" N MET K 71 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS K 77 " --> pdb=" O ARG K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 87 removed outlier: 3.596A pdb=" N GLN K 87 " --> pdb=" O ASP K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'K' and resid 103 through 119 Processing helix chain 'K' and resid 121 through 127 Processing helix chain 'K' and resid 140 through 151 removed outlier: 3.553A pdb=" N VAL K 144 " --> pdb=" O SER K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 175 removed outlier: 3.556A pdb=" N LEU K 171 " --> pdb=" O GLY K 167 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN K 172 " --> pdb=" O GLN K 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 208 removed outlier: 3.709A pdb=" N THR K 197 " --> pdb=" O LYS K 193 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG K 203 " --> pdb=" O ASP K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 234 removed outlier: 3.524A pdb=" N ARG K 229 " --> pdb=" O SER K 225 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU K 230 " --> pdb=" O GLU K 226 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG K 231 " --> pdb=" O GLU K 227 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA K 233 " --> pdb=" O ARG K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 258 removed outlier: 3.506A pdb=" N GLN K 252 " --> pdb=" O GLU K 248 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU K 255 " --> pdb=" O HIS K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 289 removed outlier: 3.521A pdb=" N THR K 289 " --> pdb=" O ASP K 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 286 through 289' Processing helix chain 'K' and resid 321 through 327 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.514A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 79 removed outlier: 3.557A pdb=" N NLE E 79 " --> pdb=" O GLN E 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 76 through 79' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.572A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.595A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.564A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.621A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.575A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.524A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.728A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.515A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 12 through 16 removed outlier: 3.624A pdb=" N PHE L 45 " --> pdb=" O LYS L 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 45 through 46 removed outlier: 7.199A pdb=" N ARG F 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'F' and resid 96 through 98 removed outlier: 6.155A pdb=" N THR F 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.062A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'G' and resid 100 through 102 removed outlier: 6.758A pdb=" N THR G 101 " --> pdb=" O TYR B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'K' and resid 6 through 7 Processing sheet with id=AA8, first strand: chain 'K' and resid 215 through 220 removed outlier: 6.479A pdb=" N HIS K 182 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N GLU K 219 " --> pdb=" O HIS K 182 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLY K 184 " --> pdb=" O GLU K 219 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE K 159 " --> pdb=" O HIS K 181 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE K 238 " --> pdb=" O VAL K 267 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.235A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 88 through 89 449 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 338 hydrogen bonds 668 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 277 stacking parallelities Total time for adding SS restraints: 5.81 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2831 1.33 - 1.45: 5088 1.45 - 1.57: 7738 1.57 - 1.69: 582 1.69 - 1.81: 48 Bond restraints: 16287 Sorted by residual: bond pdb=" C ALA F 69 " pdb=" N VAL F 70 " ideal model delta sigma weight residual 1.335 1.298 0.036 1.16e-02 7.43e+03 9.90e+00 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.499 -0.077 3.00e-02 1.11e+03 6.64e+00 bond pdb=" C2 SAM K 500 " pdb=" N3 SAM K 500 " ideal model delta sigma weight residual 1.322 1.373 -0.051 2.00e-02 2.50e+03 6.38e+00 bond pdb=" C2 SAM K 500 " pdb=" N1 SAM K 500 " ideal model delta sigma weight residual 1.329 1.378 -0.049 2.00e-02 2.50e+03 6.01e+00 bond pdb=" C8 SAM K 500 " pdb=" N7 SAM K 500 " ideal model delta sigma weight residual 1.298 1.346 -0.048 2.00e-02 2.50e+03 5.72e+00 ... (remaining 16282 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 22986 3.20 - 6.40: 221 6.40 - 9.60: 40 9.60 - 12.79: 5 12.79 - 15.99: 7 Bond angle restraints: 23259 Sorted by residual: angle pdb=" C GLU K 47 " pdb=" N ILE K 48 " pdb=" CA ILE K 48 " ideal model delta sigma weight residual 121.70 137.69 -15.99 1.80e+00 3.09e-01 7.89e+01 angle pdb=" N LEU F 37 " pdb=" CA LEU F 37 " pdb=" C LEU F 37 " ideal model delta sigma weight residual 114.75 104.75 10.00 1.26e+00 6.30e-01 6.30e+01 angle pdb=" C ARG F 67 " pdb=" N ASP F 68 " pdb=" CA ASP F 68 " ideal model delta sigma weight residual 121.54 134.44 -12.90 1.91e+00 2.74e-01 4.56e+01 angle pdb=" C PHE F 100 " pdb=" N GLY F 101 " pdb=" CA GLY F 101 " ideal model delta sigma weight residual 121.70 133.06 -11.36 1.80e+00 3.09e-01 3.98e+01 angle pdb=" CA PHE F 100 " pdb=" C PHE F 100 " pdb=" N GLY F 101 " ideal model delta sigma weight residual 119.07 125.58 -6.51 1.23e+00 6.61e-01 2.81e+01 ... (remaining 23254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 7784 35.46 - 70.91: 1291 70.91 - 106.37: 5 106.37 - 141.83: 1 141.83 - 177.28: 2 Dihedral angle restraints: 9083 sinusoidal: 5667 harmonic: 3416 Sorted by residual: dihedral pdb=" CA GLN F 27 " pdb=" C GLN F 27 " pdb=" N GLY F 28 " pdb=" CA GLY F 28 " ideal model delta harmonic sigma weight residual 180.00 116.95 63.05 0 5.00e+00 4.00e-02 1.59e+02 dihedral pdb=" CA VAL F 57 " pdb=" C VAL F 57 " pdb=" N LEU F 58 " pdb=" CA LEU F 58 " ideal model delta harmonic sigma weight residual -180.00 -138.91 -41.09 0 5.00e+00 4.00e-02 6.75e+01 dihedral pdb=" CA ASP K 32 " pdb=" C ASP K 32 " pdb=" N ALA K 33 " pdb=" CA ALA K 33 " ideal model delta harmonic sigma weight residual -180.00 -142.61 -37.39 0 5.00e+00 4.00e-02 5.59e+01 ... (remaining 9080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2296 0.073 - 0.145: 280 0.145 - 0.218: 43 0.218 - 0.290: 4 0.290 - 0.362: 3 Chirality restraints: 2626 Sorted by residual: chirality pdb=" CB ILE C 79 " pdb=" CA ILE C 79 " pdb=" CG1 ILE C 79 " pdb=" CG2 ILE C 79 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CB ILE G 79 " pdb=" CA ILE G 79 " pdb=" CG1 ILE G 79 " pdb=" CG2 ILE G 79 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CB VAL F 43 " pdb=" CA VAL F 43 " pdb=" CG1 VAL F 43 " pdb=" CG2 VAL F 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 2623 not shown) Planarity restraints: 1940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 57 " -0.021 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C VAL F 57 " 0.074 2.00e-02 2.50e+03 pdb=" O VAL F 57 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU F 58 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 25 " 0.024 2.00e-02 2.50e+03 2.15e-02 8.07e+00 pdb=" CG PHE G 25 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE G 25 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE G 25 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE G 25 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE G 25 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE G 25 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 25 " -0.024 2.00e-02 2.50e+03 2.14e-02 8.02e+00 pdb=" CG PHE C 25 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE C 25 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE C 25 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 25 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 25 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 25 " -0.008 2.00e-02 2.50e+03 ... (remaining 1937 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2351 2.76 - 3.30: 12570 3.30 - 3.83: 28453 3.83 - 4.37: 36591 4.37 - 4.90: 52210 Nonbonded interactions: 132175 Sorted by model distance: nonbonded pdb=" OG1 THR F 82 " pdb=" O MET F 84 " model vdw 2.228 3.040 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR K 154 " pdb=" OD1 ASP K 156 " model vdw 2.302 3.040 nonbonded pdb=" O GLU K 36 " pdb=" OG1 THR K 40 " model vdw 2.341 3.040 nonbonded pdb=" NH2 ARG F 78 " pdb=" OD2 ASP F 85 " model vdw 2.342 3.120 ... (remaining 132170 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' and resid 38 through 135) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 102) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'H' } 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=0.25 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 40.370 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:10.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.008 0.077 16287 Z= 0.333 Angle : 0.969 15.994 23259 Z= 0.543 Chirality : 0.053 0.362 2626 Planarity : 0.007 0.069 1940 Dihedral : 23.821 177.284 6877 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.27 % Favored : 95.56 % Rotamer: Outliers : 0.90 % Allowed : 3.40 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.89 % 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: -4.82 (0.18), residues: 1148 helix: -4.10 (0.09), residues: 665 sheet: -1.34 (0.51), residues: 80 loop : -1.44 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP K 89 HIS 0.015 0.003 HIS B 75 PHE 0.049 0.004 PHE G 25 TYR 0.031 0.003 TYR K 312 ARG 0.016 0.001 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.29077 ( 787) hydrogen bonds : angle 9.89094 ( 1982) covalent geometry : bond 0.00753 (16287) covalent geometry : angle 0.96856 (23259) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 255 time to evaluate : 1.202 Fit side-chains REVERT: F 53 GLU cc_start: 0.8495 (tp30) cc_final: 0.8279 (tp30) REVERT: H 54 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.7999 (mt) REVERT: H 71 GLU cc_start: 0.7217 (pp20) cc_final: 0.6872 (pp20) REVERT: A 50 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7951 (mt-10) REVERT: B 52 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7751 (mm-30) outliers start: 9 outliers final: 4 residues processed: 262 average time/residue: 2.0872 time to fit residues: 580.3626 Evaluate side-chains 175 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain B residue 97 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 60 ASN F 18 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 24 GLN G 82 HIS G 94 ASN G 110 ASN H 63 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 ASN K 146 GLN K 234 ASN K 324 ASN E 76 GLN E 85 GLN A 39 HIS A 68 GLN D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS C 82 HIS B 25 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.172703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.139019 restraints weight = 17435.511| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.11 r_work: 0.3550 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16287 Z= 0.171 Angle : 0.663 12.875 23259 Z= 0.383 Chirality : 0.039 0.182 2626 Planarity : 0.005 0.061 1940 Dihedral : 28.775 178.237 4538 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.48 % Favored : 96.34 % Rotamer: Outliers : 2.90 % Allowed : 10.61 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -1.78 (0.22), residues: 1148 helix: -1.20 (0.18), residues: 670 sheet: -0.77 (0.56), residues: 82 loop : -0.87 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP K 89 HIS 0.005 0.001 HIS C 82 PHE 0.019 0.002 PHE K 223 TYR 0.012 0.001 TYR F 72 ARG 0.005 0.001 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.05401 ( 787) hydrogen bonds : angle 3.43432 ( 1982) covalent geometry : bond 0.00369 (16287) covalent geometry : angle 0.66317 (23259) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 1.268 Fit side-chains revert: symmetry clash REVERT: H 71 GLU cc_start: 0.7867 (pp20) cc_final: 0.7529 (pp20) REVERT: K 323 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6673 (mp0) REVERT: A 50 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8377 (mt-10) REVERT: D 99 ARG cc_start: 0.8545 (mtt90) cc_final: 0.8340 (mtt180) REVERT: B 79 LYS cc_start: 0.8977 (mtpp) cc_final: 0.8431 (mppt) outliers start: 29 outliers final: 13 residues processed: 197 average time/residue: 1.8341 time to fit residues: 387.0023 Evaluate side-chains 172 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 51 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 125 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 109 HIS D 47 GLN ** D 84 ASN ** 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 = 0.4068 r_free = 0.4068 target = 0.168397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.134414 restraints weight = 17427.993| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.14 r_work: 0.3476 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16287 Z= 0.222 Angle : 0.674 12.678 23259 Z= 0.387 Chirality : 0.041 0.196 2626 Planarity : 0.005 0.054 1940 Dihedral : 28.811 175.795 4536 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.82 % Rotamer: Outliers : 3.20 % Allowed : 12.21 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -0.30 (0.25), residues: 1148 helix: 0.13 (0.20), residues: 679 sheet: -0.22 (0.59), residues: 81 loop : -0.55 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP K 205 HIS 0.006 0.001 HIS F 75 PHE 0.019 0.002 PHE C 25 TYR 0.017 0.002 TYR F 72 ARG 0.004 0.001 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.05488 ( 787) hydrogen bonds : angle 3.16761 ( 1982) covalent geometry : bond 0.00501 (16287) covalent geometry : angle 0.67371 (23259) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7919 (mt) REVERT: H 71 GLU cc_start: 0.7838 (pp20) cc_final: 0.7516 (pp20) REVERT: K 206 MET cc_start: 0.8368 (mmt) cc_final: 0.7832 (mmt) REVERT: K 323 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6677 (mp0) REVERT: A 50 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8347 (mt-10) REVERT: D 99 ARG cc_start: 0.8609 (mtt90) cc_final: 0.8369 (mtt180) REVERT: C 64 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8201 (tt0) outliers start: 32 outliers final: 20 residues processed: 188 average time/residue: 1.8003 time to fit residues: 362.2387 Evaluate side-chains 186 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 1 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 0.0000 chunk 49 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 84 ASN H 109 HIS E 125 GLN D 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.169217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.135272 restraints weight = 17341.908| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.09 r_work: 0.3498 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16287 Z= 0.200 Angle : 0.637 12.643 23259 Z= 0.368 Chirality : 0.040 0.193 2626 Planarity : 0.005 0.055 1940 Dihedral : 28.746 177.523 4536 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.83 % Favored : 95.99 % Rotamer: Outliers : 2.50 % Allowed : 13.31 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: 0.30 (0.25), residues: 1148 helix: 0.65 (0.20), residues: 679 sheet: -0.03 (0.59), residues: 81 loop : -0.36 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP K 205 HIS 0.005 0.001 HIS K 315 PHE 0.015 0.002 PHE K 223 TYR 0.012 0.001 TYR F 72 ARG 0.006 0.001 ARG H 79 Details of bonding type rmsd hydrogen bonds : bond 0.04933 ( 787) hydrogen bonds : angle 3.01846 ( 1982) covalent geometry : bond 0.00448 (16287) covalent geometry : angle 0.63702 (23259) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 1.280 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7950 (mt) REVERT: G 75 LYS cc_start: 0.9023 (mmtp) cc_final: 0.8560 (mmtm) REVERT: H 54 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8513 (tt) REVERT: H 71 GLU cc_start: 0.7775 (pp20) cc_final: 0.7507 (pp20) REVERT: K 323 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6702 (mp0) REVERT: A 50 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8288 (mt-10) outliers start: 25 outliers final: 19 residues processed: 186 average time/residue: 1.8614 time to fit residues: 370.3445 Evaluate side-chains 185 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 109 HIS E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.170395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.136678 restraints weight = 17624.979| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.09 r_work: 0.3507 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16287 Z= 0.160 Angle : 0.618 12.684 23259 Z= 0.359 Chirality : 0.038 0.187 2626 Planarity : 0.004 0.053 1940 Dihedral : 28.741 178.027 4536 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.92 % Favored : 95.91 % Rotamer: Outliers : 3.10 % Allowed : 13.61 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: 0.64 (0.25), residues: 1148 helix: 0.94 (0.21), residues: 677 sheet: 0.05 (0.59), residues: 81 loop : -0.24 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP K 205 HIS 0.005 0.001 HIS K 315 PHE 0.014 0.001 PHE K 223 TYR 0.012 0.001 TYR D 40 ARG 0.006 0.000 ARG H 79 Details of bonding type rmsd hydrogen bonds : bond 0.04582 ( 787) hydrogen bonds : angle 2.98253 ( 1982) covalent geometry : bond 0.00348 (16287) covalent geometry : angle 0.61832 (23259) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7900 (mt) REVERT: G 75 LYS cc_start: 0.9024 (mmtp) cc_final: 0.8566 (mmtm) REVERT: H 71 GLU cc_start: 0.7764 (pp20) cc_final: 0.7484 (pp20) REVERT: K 323 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6687 (mp0) REVERT: A 50 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8290 (mt-10) REVERT: D 71 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: C 15 LYS cc_start: 0.8086 (mtpp) cc_final: 0.7829 (mtpm) REVERT: C 64 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8185 (tt0) outliers start: 31 outliers final: 22 residues processed: 183 average time/residue: 1.8822 time to fit residues: 368.9925 Evaluate side-chains 188 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 102 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 91 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 80 optimal weight: 0.5980 chunk 75 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 109 HIS E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.166937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.132977 restraints weight = 17489.825| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.13 r_work: 0.3460 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16287 Z= 0.266 Angle : 0.677 12.637 23259 Z= 0.389 Chirality : 0.043 0.202 2626 Planarity : 0.005 0.050 1940 Dihedral : 28.927 176.168 4534 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.27 % Favored : 95.56 % Rotamer: Outliers : 3.20 % Allowed : 13.71 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1148 helix: 0.94 (0.21), residues: 679 sheet: 0.12 (0.60), residues: 80 loop : -0.28 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP K 205 HIS 0.007 0.001 HIS F 75 PHE 0.016 0.002 PHE K 223 TYR 0.012 0.002 TYR F 88 ARG 0.006 0.001 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.05642 ( 787) hydrogen bonds : angle 3.08889 ( 1982) covalent geometry : bond 0.00609 (16287) covalent geometry : angle 0.67686 (23259) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8056 (mt) REVERT: K 206 MET cc_start: 0.8439 (mmt) cc_final: 0.7956 (mmt) REVERT: A 50 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8344 (mt-10) REVERT: D 71 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: C 64 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8261 (tt0) outliers start: 32 outliers final: 24 residues processed: 185 average time/residue: 2.3212 time to fit residues: 460.8900 Evaluate side-chains 187 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 58 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 30.0000 chunk 87 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 40 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 109 HIS E 39 HIS E 125 GLN C 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.168690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.134885 restraints weight = 17523.912| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.08 r_work: 0.3493 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16287 Z= 0.168 Angle : 0.639 12.667 23259 Z= 0.371 Chirality : 0.039 0.181 2626 Planarity : 0.004 0.052 1940 Dihedral : 28.922 176.698 4532 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.82 % Rotamer: Outliers : 2.90 % Allowed : 14.71 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: 0.83 (0.26), residues: 1148 helix: 1.11 (0.21), residues: 679 sheet: 0.18 (0.60), residues: 80 loop : -0.21 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 205 HIS 0.004 0.001 HIS B 75 PHE 0.014 0.001 PHE K 223 TYR 0.014 0.001 TYR D 40 ARG 0.004 0.000 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.04877 ( 787) hydrogen bonds : angle 3.02724 ( 1982) covalent geometry : bond 0.00369 (16287) covalent geometry : angle 0.63895 (23259) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7972 (mt) REVERT: H 71 GLU cc_start: 0.7769 (pp20) cc_final: 0.7499 (pp20) REVERT: K 206 MET cc_start: 0.8406 (mmt) cc_final: 0.7859 (mmt) REVERT: K 323 GLU cc_start: 0.6748 (mm-30) cc_final: 0.6494 (mp0) REVERT: A 50 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8297 (mt-10) REVERT: D 71 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: C 64 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8206 (tt0) outliers start: 29 outliers final: 22 residues processed: 182 average time/residue: 2.4431 time to fit residues: 476.8990 Evaluate side-chains 186 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.0970 chunk 102 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 39 optimal weight: 30.0000 chunk 32 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 109 HIS E 125 GLN C 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.166796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.132985 restraints weight = 17294.660| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.09 r_work: 0.3464 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 16287 Z= 0.255 Angle : 0.671 12.647 23259 Z= 0.386 Chirality : 0.042 0.196 2626 Planarity : 0.005 0.050 1940 Dihedral : 28.918 176.212 4532 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.18 % Favored : 95.64 % Rotamer: Outliers : 3.40 % Allowed : 14.51 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: 0.76 (0.25), residues: 1148 helix: 1.06 (0.21), residues: 679 sheet: 0.15 (0.60), residues: 80 loop : -0.26 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP K 205 HIS 0.007 0.001 HIS F 75 PHE 0.015 0.002 PHE K 223 TYR 0.011 0.002 TYR F 72 ARG 0.007 0.001 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.05590 ( 787) hydrogen bonds : angle 3.07186 ( 1982) covalent geometry : bond 0.00583 (16287) covalent geometry : angle 0.67060 (23259) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 2.385 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8042 (mt) REVERT: G 20 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8241 (ptp-170) REVERT: A 50 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8324 (mt-10) REVERT: D 71 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: C 64 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: C 95 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8571 (ttmt) outliers start: 34 outliers final: 24 residues processed: 179 average time/residue: 3.1766 time to fit residues: 615.8732 Evaluate side-chains 187 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 39 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 109 HIS E 125 GLN D 67 ASN C 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.167675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.133812 restraints weight = 17376.106| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.07 r_work: 0.3474 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16287 Z= 0.187 Angle : 0.647 12.699 23259 Z= 0.374 Chirality : 0.040 0.186 2626 Planarity : 0.005 0.051 1940 Dihedral : 28.935 176.310 4532 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.09 % Favored : 95.73 % Rotamer: Outliers : 3.40 % Allowed : 14.81 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: 0.88 (0.26), residues: 1148 helix: 1.16 (0.21), residues: 679 sheet: 0.18 (0.60), residues: 80 loop : -0.22 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 205 HIS 0.005 0.001 HIS F 75 PHE 0.013 0.001 PHE K 223 TYR 0.013 0.001 TYR D 40 ARG 0.005 0.000 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.05203 ( 787) hydrogen bonds : angle 3.04195 ( 1982) covalent geometry : bond 0.00414 (16287) covalent geometry : angle 0.64704 (23259) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8028 (mt) REVERT: G 20 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8197 (ptp-170) REVERT: K 323 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6521 (mp0) REVERT: A 50 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8301 (mt-10) REVERT: D 67 ASN cc_start: 0.9043 (m-40) cc_final: 0.8819 (m110) REVERT: D 71 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: C 64 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8224 (tt0) REVERT: C 95 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8534 (ttmt) outliers start: 34 outliers final: 24 residues processed: 186 average time/residue: 1.9921 time to fit residues: 398.7888 Evaluate side-chains 191 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 42 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 91 optimal weight: 0.0370 chunk 61 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 109 HIS E 125 GLN C 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.167829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.133925 restraints weight = 17628.955| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.08 r_work: 0.3476 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16287 Z= 0.200 Angle : 0.644 12.663 23259 Z= 0.372 Chirality : 0.040 0.185 2626 Planarity : 0.005 0.064 1940 Dihedral : 28.907 176.937 4532 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.09 % Favored : 95.73 % Rotamer: Outliers : 2.80 % Allowed : 15.42 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: 0.91 (0.26), residues: 1148 helix: 1.18 (0.21), residues: 679 sheet: 0.19 (0.60), residues: 80 loop : -0.20 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 205 HIS 0.005 0.001 HIS K 315 PHE 0.014 0.001 PHE K 223 TYR 0.012 0.001 TYR F 72 ARG 0.006 0.000 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.05037 ( 787) hydrogen bonds : angle 3.00785 ( 1982) covalent geometry : bond 0.00451 (16287) covalent geometry : angle 0.64386 (23259) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8021 (mt) REVERT: G 20 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8198 (ptp-170) REVERT: K 323 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6524 (mp0) REVERT: A 50 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8308 (mt-10) REVERT: D 71 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: C 64 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8227 (tt0) outliers start: 28 outliers final: 23 residues processed: 176 average time/residue: 1.7859 time to fit residues: 336.4288 Evaluate side-chains 184 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 109 HIS E 125 GLN C 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.168300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.134521 restraints weight = 17495.522| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.07 r_work: 0.3484 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16287 Z= 0.180 Angle : 0.635 12.707 23259 Z= 0.368 Chirality : 0.039 0.181 2626 Planarity : 0.005 0.051 1940 Dihedral : 28.902 177.002 4532 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.09 % Favored : 95.73 % Rotamer: Outliers : 2.90 % Allowed : 15.32 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: 0.98 (0.26), residues: 1148 helix: 1.24 (0.21), residues: 679 sheet: 0.21 (0.60), residues: 80 loop : -0.17 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 205 HIS 0.004 0.001 HIS K 315 PHE 0.014 0.001 PHE K 223 TYR 0.013 0.001 TYR D 40 ARG 0.005 0.000 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.04873 ( 787) hydrogen bonds : angle 2.99761 ( 1982) covalent geometry : bond 0.00399 (16287) covalent geometry : angle 0.63462 (23259) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16651.93 seconds wall clock time: 296 minutes 46.81 seconds (17806.81 seconds total)