Starting phenix.real_space_refine on Wed Jul 30 11:10:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ukh_26581/07_2025/7ukh_26581.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ukh_26581/07_2025/7ukh_26581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ukh_26581/07_2025/7ukh_26581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ukh_26581/07_2025/7ukh_26581.map" model { file = "/net/cci-nas-00/data/ceres_data/7ukh_26581/07_2025/7ukh_26581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ukh_26581/07_2025/7ukh_26581.cif" } resolution = 2.33 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= -0.003 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 12 9.91 5 Zn 4 6.06 5 S 68 5.16 5 C 7800 2.51 5 N 2116 2.21 5 O 2340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12340 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1612 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 11, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 47 Chain: "I" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1469 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 176} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1019 SG CYS A 132 81.658 84.010 41.310 1.00 20.30 S ATOM 1025 SG CYS A 133 80.730 80.238 41.398 1.00 17.59 S Restraints were copied for chains: K, J, L, C, B, D Time building chain proxies: 7.73, per 1000 atoms: 0.63 Number of scatterers: 12340 At special positions: 0 Unit cell: (142.898, 142.898, 62.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 Ca 12 19.99 S 68 16.00 O 2340 8.00 N 2116 7.00 C 7800 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: 3.04 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" ND1 HIS A 105 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 133 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 132 " pdb="ZN ZN A 901 " - pdb=" SG CYS B 111 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" ND1 HIS B 105 " pdb="ZN ZN B 901 " - pdb=" SG CYS B 133 " pdb="ZN ZN B 901 " - pdb=" SG CYS B 132 " pdb="ZN ZN B 901 " - pdb=" SG CYS C 111 " pdb=" ZN C 901 " pdb="ZN ZN C 901 " - pdb=" ND1 HIS C 105 " pdb="ZN ZN C 901 " - pdb=" SG CYS D 111 " pdb="ZN ZN C 901 " - pdb=" SG CYS C 133 " pdb="ZN ZN C 901 " - pdb=" SG CYS C 132 " pdb=" ZN D 901 " pdb="ZN ZN D 901 " - pdb=" ND1 HIS D 105 " pdb="ZN ZN D 901 " - pdb=" SG CYS A 111 " pdb="ZN ZN D 901 " - pdb=" SG CYS D 133 " pdb="ZN ZN D 901 " - pdb=" SG CYS D 132 " Number of angles added : 12 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2912 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 68.5% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 Processing helix chain 'A' and resid 17 through 19 No H-bonds generated for 'chain 'A' and resid 17 through 19' Processing helix chain 'A' and resid 35 through 39 removed outlier: 3.752A pdb=" N GLN A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.501A pdb=" N LEU A 59 " --> pdb=" O TRP A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 88 through 102 removed outlier: 4.007A pdb=" N HIS A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 130 through 153 removed outlier: 4.603A pdb=" N GLU A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N GLU A 136 " --> pdb=" O CYS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 451 Processing helix chain 'A' and resid 473 through 490 Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'B' and resid 17 through 19 No H-bonds generated for 'chain 'B' and resid 17 through 19' Processing helix chain 'B' and resid 35 through 39 removed outlier: 3.751A pdb=" N GLN B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.501A pdb=" N LEU B 59 " --> pdb=" O TRP B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 88 through 102 removed outlier: 4.007A pdb=" N HIS B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 130 through 153 removed outlier: 4.603A pdb=" N GLU B 135 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N GLU B 136 " --> pdb=" O CYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 451 Processing helix chain 'B' and resid 473 through 490 Processing helix chain 'C' and resid 8 through 16 Processing helix chain 'C' and resid 17 through 19 No H-bonds generated for 'chain 'C' and resid 17 through 19' Processing helix chain 'C' and resid 35 through 39 removed outlier: 3.751A pdb=" N GLN C 39 " --> pdb=" O LYS C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.501A pdb=" N LEU C 59 " --> pdb=" O TRP C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'C' and resid 88 through 102 removed outlier: 4.007A pdb=" N HIS C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 130 through 153 removed outlier: 4.603A pdb=" N GLU C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLU C 136 " --> pdb=" O CYS C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 451 Processing helix chain 'C' and resid 473 through 490 Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 17 through 19 No H-bonds generated for 'chain 'D' and resid 17 through 19' Processing helix chain 'D' and resid 35 through 39 removed outlier: 3.752A pdb=" N GLN D 39 " --> pdb=" O LYS D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 69 through 74 Processing helix chain 'D' and resid 88 through 102 removed outlier: 4.007A pdb=" N HIS D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 122 Processing helix chain 'D' and resid 125 through 129 Processing helix chain 'D' and resid 130 through 153 removed outlier: 4.603A pdb=" N GLU D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLU D 136 " --> pdb=" O CYS D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 451 Processing helix chain 'D' and resid 473 through 490 Processing helix chain 'I' and resid 74 through 82 Processing helix chain 'I' and resid 85 through 100 Processing helix chain 'I' and resid 107 through 116 removed outlier: 3.973A pdb=" N GLN I 116 " --> pdb=" O GLN I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 135 Processing helix chain 'I' and resid 144 through 157 Processing helix chain 'I' and resid 158 through 171 Processing helix chain 'I' and resid 179 through 195 removed outlier: 3.762A pdb=" N MET I 193 " --> pdb=" O SER I 189 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET I 194 " --> pdb=" O ILE I 190 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY I 195 " --> pdb=" O TYR I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 219 Processing helix chain 'I' and resid 228 through 237 Processing helix chain 'I' and resid 238 through 252 removed outlier: 3.631A pdb=" N ASP I 249 " --> pdb=" O MET I 245 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN I 250 " --> pdb=" O GLN I 246 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE I 252 " --> pdb=" O PHE I 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 82 Processing helix chain 'J' and resid 85 through 100 Processing helix chain 'J' and resid 107 through 116 removed outlier: 3.974A pdb=" N GLN J 116 " --> pdb=" O GLN J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 135 Processing helix chain 'J' and resid 144 through 157 Processing helix chain 'J' and resid 158 through 171 Processing helix chain 'J' and resid 179 through 195 removed outlier: 3.762A pdb=" N MET J 193 " --> pdb=" O SER J 189 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET J 194 " --> pdb=" O ILE J 190 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY J 195 " --> pdb=" O TYR J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 219 Processing helix chain 'J' and resid 228 through 237 Processing helix chain 'J' and resid 238 through 252 removed outlier: 3.632A pdb=" N ASP J 249 " --> pdb=" O MET J 245 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN J 250 " --> pdb=" O GLN J 246 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE J 252 " --> pdb=" O PHE J 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 82 Processing helix chain 'K' and resid 85 through 100 Processing helix chain 'K' and resid 107 through 116 removed outlier: 3.973A pdb=" N GLN K 116 " --> pdb=" O GLN K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 135 Processing helix chain 'K' and resid 144 through 157 Processing helix chain 'K' and resid 158 through 171 Processing helix chain 'K' and resid 179 through 195 removed outlier: 3.761A pdb=" N MET K 193 " --> pdb=" O SER K 189 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET K 194 " --> pdb=" O ILE K 190 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY K 195 " --> pdb=" O TYR K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 219 Processing helix chain 'K' and resid 228 through 237 Processing helix chain 'K' and resid 238 through 252 removed outlier: 3.631A pdb=" N ASP K 249 " --> pdb=" O MET K 245 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN K 250 " --> pdb=" O GLN K 246 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE K 252 " --> pdb=" O PHE K 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 82 Processing helix chain 'L' and resid 85 through 100 Processing helix chain 'L' and resid 107 through 116 removed outlier: 3.974A pdb=" N GLN L 116 " --> pdb=" O GLN L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 135 Processing helix chain 'L' and resid 144 through 157 Processing helix chain 'L' and resid 158 through 171 Processing helix chain 'L' and resid 179 through 195 removed outlier: 3.761A pdb=" N MET L 193 " --> pdb=" O SER L 189 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET L 194 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY L 195 " --> pdb=" O TYR L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 219 Processing helix chain 'L' and resid 228 through 237 Processing helix chain 'L' and resid 238 through 252 removed outlier: 3.632A pdb=" N ASP L 249 " --> pdb=" O MET L 245 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN L 250 " --> pdb=" O GLN L 246 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE L 252 " --> pdb=" O PHE L 248 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 54 Processing sheet with id=AA2, first strand: chain 'B' and resid 50 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 50 through 54 Processing sheet with id=AA4, first strand: chain 'D' and resid 50 through 54 Processing sheet with id=AA5, first strand: chain 'I' and resid 104 through 106 Processing sheet with id=AA6, first strand: chain 'I' and resid 177 through 178 Processing sheet with id=AA7, first strand: chain 'J' and resid 104 through 106 Processing sheet with id=AA8, first strand: chain 'J' and resid 177 through 178 Processing sheet with id=AA9, first strand: chain 'K' and resid 104 through 106 Processing sheet with id=AB1, first strand: chain 'K' and resid 177 through 178 Processing sheet with id=AB2, first strand: chain 'L' and resid 104 through 106 Processing sheet with id=AB3, first strand: chain 'L' and resid 177 through 178 741 hydrogen bonds defined for protein. 2103 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.77 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4093 1.34 - 1.46: 2000 1.46 - 1.57: 6419 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 12620 Sorted by residual: bond pdb=" N ALA A 145 " pdb=" CA ALA A 145 " ideal model delta sigma weight residual 1.459 1.483 -0.023 1.21e-02 6.83e+03 3.76e+00 bond pdb=" N ALA D 145 " pdb=" CA ALA D 145 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.21e-02 6.83e+03 3.68e+00 bond pdb=" N ALA C 145 " pdb=" CA ALA C 145 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.21e-02 6.83e+03 3.56e+00 bond pdb=" N ALA B 145 " pdb=" CA ALA B 145 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.21e-02 6.83e+03 3.38e+00 bond pdb=" C ASN D 144 " pdb=" N ALA D 145 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.31e-02 5.83e+03 1.83e+00 ... (remaining 12615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 16138 1.19 - 2.39: 744 2.39 - 3.58: 112 3.58 - 4.78: 22 4.78 - 5.97: 28 Bond angle restraints: 17044 Sorted by residual: angle pdb=" CA TRP C 19 " pdb=" CB TRP C 19 " pdb=" CG TRP C 19 " ideal model delta sigma weight residual 113.60 117.74 -4.14 1.90e+00 2.77e-01 4.74e+00 angle pdb=" CA TRP D 19 " pdb=" CB TRP D 19 " pdb=" CG TRP D 19 " ideal model delta sigma weight residual 113.60 117.71 -4.11 1.90e+00 2.77e-01 4.69e+00 angle pdb=" CA TRP B 19 " pdb=" CB TRP B 19 " pdb=" CG TRP B 19 " ideal model delta sigma weight residual 113.60 117.69 -4.09 1.90e+00 2.77e-01 4.64e+00 angle pdb=" CA TRP A 19 " pdb=" CB TRP A 19 " pdb=" CG TRP A 19 " ideal model delta sigma weight residual 113.60 117.69 -4.09 1.90e+00 2.77e-01 4.64e+00 angle pdb=" O ASN C 144 " pdb=" C ASN C 144 " pdb=" N ALA C 145 " ideal model delta sigma weight residual 122.27 120.04 2.23 1.23e+00 6.61e-01 3.28e+00 ... (remaining 17039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 6518 17.84 - 35.67: 690 35.67 - 53.51: 236 53.51 - 71.35: 52 71.35 - 89.18: 32 Dihedral angle restraints: 7528 sinusoidal: 3032 harmonic: 4496 Sorted by residual: dihedral pdb=" CB GLU K 145 " pdb=" CG GLU K 145 " pdb=" CD GLU K 145 " pdb=" OE1 GLU K 145 " ideal model delta sinusoidal sigma weight residual 0.00 -89.18 89.18 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU I 145 " pdb=" CG GLU I 145 " pdb=" CD GLU I 145 " pdb=" OE1 GLU I 145 " ideal model delta sinusoidal sigma weight residual 0.00 -89.18 89.18 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU J 145 " pdb=" CG GLU J 145 " pdb=" CD GLU J 145 " pdb=" OE1 GLU J 145 " ideal model delta sinusoidal sigma weight residual 0.00 -89.14 89.14 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 7525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 948 0.028 - 0.057: 513 0.057 - 0.085: 182 0.085 - 0.114: 107 0.114 - 0.142: 18 Chirality restraints: 1768 Sorted by residual: chirality pdb=" CG LEU K 163 " pdb=" CB LEU K 163 " pdb=" CD1 LEU K 163 " pdb=" CD2 LEU K 163 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CG LEU L 163 " pdb=" CB LEU L 163 " pdb=" CD1 LEU L 163 " pdb=" CD2 LEU L 163 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CG LEU I 163 " pdb=" CB LEU I 163 " pdb=" CD1 LEU I 163 " pdb=" CD2 LEU I 163 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 1765 not shown) Planarity restraints: 2264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 144 " 0.016 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C ASN C 144 " -0.053 2.00e-02 2.50e+03 pdb=" O ASN C 144 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA C 145 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 144 " 0.016 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C ASN B 144 " -0.053 2.00e-02 2.50e+03 pdb=" O ASN B 144 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA B 145 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 144 " 0.016 2.00e-02 2.50e+03 3.04e-02 9.24e+00 pdb=" C ASN D 144 " -0.053 2.00e-02 2.50e+03 pdb=" O ASN D 144 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA D 145 " 0.018 2.00e-02 2.50e+03 ... (remaining 2261 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 247 2.61 - 3.18: 11232 3.18 - 3.75: 20579 3.75 - 4.33: 29414 4.33 - 4.90: 45684 Nonbonded interactions: 107156 Sorted by model distance: nonbonded pdb=" OD1 ASP J 135 " pdb=" O SER J 141 " model vdw 2.035 3.040 nonbonded pdb=" OD1 ASP I 135 " pdb=" O SER I 141 " model vdw 2.036 3.040 nonbonded pdb=" OD1 ASP K 135 " pdb=" O SER K 141 " model vdw 2.036 3.040 nonbonded pdb=" OD1 ASP L 135 " pdb=" O SER L 141 " model vdw 2.036 3.040 nonbonded pdb=" OD1 ASP K 219 " pdb="CA CA K 903 " model vdw 2.170 2.510 ... (remaining 107151 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: 0.09 Found NCS groups: ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 197.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 32.460 Find NCS groups from input model: 0.260 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: 0.000 Load rotamer database and sin/cos tables:14.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 245.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12636 Z= 0.200 Angle : 0.613 5.974 17056 Z= 0.350 Chirality : 0.043 0.142 1768 Planarity : 0.004 0.034 2264 Dihedral : 17.880 89.183 4616 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.80 % Allowed : 18.05 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.22), residues: 1504 helix: 1.15 (0.17), residues: 968 sheet: -0.43 (0.86), residues: 40 loop : -0.07 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 19 HIS 0.005 0.001 HIS B 77 PHE 0.018 0.002 PHE D 84 TYR 0.014 0.002 TYR L 126 ARG 0.003 0.001 ARG B 434 Details of bonding type rmsd hydrogen bonds : bond 0.11678 ( 741) hydrogen bonds : angle 6.06790 ( 2103) metal coordination : bond 0.02291 ( 16) metal coordination : angle 2.67425 ( 12) covalent geometry : bond 0.00425 (12620) covalent geometry : angle 0.60862 (17044) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 241 time to evaluate : 1.343 Fit side-chains outliers start: 23 outliers final: 10 residues processed: 258 average time/residue: 1.6007 time to fit residues: 440.0433 Evaluate side-chains 237 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 227 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 234 SER Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 234 SER Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 234 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 477 GLN B 56 GLN B 477 GLN C 56 GLN C 477 GLN D 56 GLN D 477 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.173679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.118872 restraints weight = 12959.861| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.99 r_work: 0.3306 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 12636 Z= 0.255 Angle : 0.637 6.325 17056 Z= 0.343 Chirality : 0.046 0.137 1768 Planarity : 0.006 0.044 2264 Dihedral : 4.780 33.737 1688 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.38 % Allowed : 17.19 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.22), residues: 1504 helix: 1.11 (0.16), residues: 968 sheet: -1.13 (0.79), residues: 40 loop : -0.01 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 19 HIS 0.007 0.002 HIS D 77 PHE 0.027 0.003 PHE L 118 TYR 0.015 0.002 TYR B 444 ARG 0.006 0.001 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.06134 ( 741) hydrogen bonds : angle 5.27487 ( 2103) metal coordination : bond 0.00614 ( 16) metal coordination : angle 2.55369 ( 12) covalent geometry : bond 0.00572 (12620) covalent geometry : angle 0.63323 (17044) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 235 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6184 (mtt90) REVERT: A 429 ARG cc_start: 0.6675 (mpt180) cc_final: 0.6408 (mpt180) REVERT: B 100 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6181 (mtt90) REVERT: C 100 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6161 (mtt90) REVERT: D 100 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6139 (mtt90) REVERT: I 77 GLN cc_start: 0.7035 (mt0) cc_final: 0.6786 (mm-40) REVERT: I 209 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6973 (mt-10) REVERT: I 212 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8078 (mm-30) REVERT: J 108 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: J 209 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6952 (mt-10) REVERT: L 77 GLN cc_start: 0.7012 (mt0) cc_final: 0.6686 (mm-40) outliers start: 56 outliers final: 22 residues processed: 260 average time/residue: 1.7093 time to fit residues: 472.6220 Evaluate side-chains 254 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain J residue 77 GLN Chi-restraints excluded: chain J residue 108 GLU Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 209 GLU Chi-restraints excluded: chain J residue 217 LYS Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain J residue 232 ILE Chi-restraints excluded: chain J residue 236 GLN Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 236 GLN Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 209 GLU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 226 VAL Chi-restraints excluded: chain L residue 232 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 135 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 147 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 52 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 477 GLN B 56 GLN B 477 GLN C 56 GLN C 477 GLN D 56 GLN D 477 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.177652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.123765 restraints weight = 13121.425| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.02 r_work: 0.3373 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12636 Z= 0.125 Angle : 0.498 5.236 17056 Z= 0.266 Chirality : 0.040 0.126 1768 Planarity : 0.004 0.026 2264 Dihedral : 4.405 34.439 1680 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.36 % Allowed : 18.59 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.22), residues: 1504 helix: 1.48 (0.17), residues: 968 sheet: -0.39 (0.89), residues: 40 loop : 0.04 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 19 HIS 0.003 0.001 HIS B 77 PHE 0.013 0.002 PHE A 84 TYR 0.009 0.001 TYR K 197 ARG 0.003 0.000 ARG B 429 Details of bonding type rmsd hydrogen bonds : bond 0.04514 ( 741) hydrogen bonds : angle 4.96654 ( 2103) metal coordination : bond 0.00404 ( 16) metal coordination : angle 2.50292 ( 12) covalent geometry : bond 0.00263 (12620) covalent geometry : angle 0.49370 (17044) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 240 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 242 MET cc_start: 0.5822 (tpp) cc_final: 0.5509 (tpp) REVERT: J 217 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7478 (tmtt) REVERT: L 77 GLN cc_start: 0.6992 (mt0) cc_final: 0.6687 (mm-40) outliers start: 43 outliers final: 20 residues processed: 261 average time/residue: 1.6617 time to fit residues: 460.6331 Evaluate side-chains 241 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 220 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 217 LYS Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 236 GLN Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 236 GLN Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 225 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 82 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 477 GLN B 56 GLN B 477 GLN C 56 GLN C 81 GLN C 477 GLN D 56 GLN D 81 GLN D 477 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.177287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.122815 restraints weight = 13045.911| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.89 r_work: 0.3368 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12636 Z= 0.139 Angle : 0.503 5.192 17056 Z= 0.269 Chirality : 0.040 0.126 1768 Planarity : 0.004 0.025 2264 Dihedral : 4.289 34.367 1680 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.59 % Allowed : 18.59 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.23), residues: 1504 helix: 1.60 (0.17), residues: 968 sheet: -0.35 (0.88), residues: 40 loop : -0.00 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 19 HIS 0.003 0.001 HIS B 94 PHE 0.015 0.002 PHE I 118 TYR 0.009 0.001 TYR C 106 ARG 0.003 0.000 ARG A 429 Details of bonding type rmsd hydrogen bonds : bond 0.04607 ( 741) hydrogen bonds : angle 4.87293 ( 2103) metal coordination : bond 0.00445 ( 16) metal coordination : angle 2.20812 ( 12) covalent geometry : bond 0.00302 (12620) covalent geometry : angle 0.49995 (17044) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 227 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8210 (pm20) REVERT: I 209 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6890 (mp0) REVERT: I 242 MET cc_start: 0.5749 (tpp) cc_final: 0.5545 (tpp) REVERT: J 209 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: J 217 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7526 (tmtt) REVERT: K 160 ASP cc_start: 0.8004 (m-30) cc_final: 0.7314 (t70) REVERT: L 77 GLN cc_start: 0.7007 (mt0) cc_final: 0.6768 (mm-40) REVERT: L 209 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: L 217 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7261 (tmtt) outliers start: 46 outliers final: 23 residues processed: 255 average time/residue: 1.6613 time to fit residues: 450.5518 Evaluate side-chains 252 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 236 GLN Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 209 GLU Chi-restraints excluded: chain J residue 217 LYS Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 236 GLN Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 236 GLN Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 209 GLU Chi-restraints excluded: chain L residue 217 LYS Chi-restraints excluded: chain L residue 225 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 89 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 3 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 477 GLN B 56 GLN B 477 GLN C 56 GLN C 81 GLN C 477 GLN D 56 GLN D 81 GLN D 477 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.176682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.122188 restraints weight = 13036.755| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.10 r_work: 0.3340 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12636 Z= 0.151 Angle : 0.513 5.223 17056 Z= 0.274 Chirality : 0.041 0.128 1768 Planarity : 0.004 0.028 2264 Dihedral : 4.293 35.193 1680 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.45 % Allowed : 17.89 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.23), residues: 1504 helix: 1.61 (0.17), residues: 968 sheet: -0.53 (0.86), residues: 40 loop : -0.04 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 19 HIS 0.004 0.001 HIS D 77 PHE 0.016 0.002 PHE K 118 TYR 0.010 0.002 TYR B 106 ARG 0.003 0.000 ARG D 429 Details of bonding type rmsd hydrogen bonds : bond 0.04706 ( 741) hydrogen bonds : angle 4.87728 ( 2103) metal coordination : bond 0.00437 ( 16) metal coordination : angle 2.18374 ( 12) covalent geometry : bond 0.00331 (12620) covalent geometry : angle 0.51023 (17044) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 229 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8146 (pm20) REVERT: B 79 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8231 (pm20) REVERT: C 79 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8248 (pm20) REVERT: D 79 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8226 (pm20) REVERT: I 209 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: I 217 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7604 (tmtt) REVERT: J 108 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: J 209 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: J 217 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7431 (tmtt) REVERT: K 108 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: K 160 ASP cc_start: 0.7973 (m-30) cc_final: 0.7273 (t70) REVERT: L 77 GLN cc_start: 0.6978 (mt0) cc_final: 0.6769 (mm-40) REVERT: L 87 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8217 (mmmt) REVERT: L 209 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: L 217 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7259 (tmtt) outliers start: 57 outliers final: 32 residues processed: 263 average time/residue: 1.6705 time to fit residues: 468.6435 Evaluate side-chains 272 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 227 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain I residue 217 LYS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 236 GLN Chi-restraints excluded: chain J residue 108 GLU Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 209 GLU Chi-restraints excluded: chain J residue 217 LYS Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 236 GLN Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 236 GLN Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 209 GLU Chi-restraints excluded: chain L residue 217 LYS Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 150 optimal weight: 0.8980 chunk 86 optimal weight: 0.0870 chunk 147 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 136 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 477 GLN B 56 GLN B 477 GLN C 56 GLN C 81 GLN C 477 GLN D 56 GLN D 81 GLN D 477 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.178093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.124462 restraints weight = 13251.543| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.13 r_work: 0.3367 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12636 Z= 0.126 Angle : 0.492 6.124 17056 Z= 0.261 Chirality : 0.040 0.127 1768 Planarity : 0.004 0.024 2264 Dihedral : 4.189 34.842 1680 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.06 % Allowed : 18.20 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.23), residues: 1504 helix: 1.67 (0.17), residues: 968 sheet: -0.20 (0.89), residues: 40 loop : -0.01 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 19 HIS 0.003 0.001 HIS D 94 PHE 0.014 0.002 PHE D 84 TYR 0.021 0.001 TYR K 197 ARG 0.003 0.000 ARG D 429 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 741) hydrogen bonds : angle 4.79657 ( 2103) metal coordination : bond 0.00403 ( 16) metal coordination : angle 2.15164 ( 12) covalent geometry : bond 0.00271 (12620) covalent geometry : angle 0.48849 (17044) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 235 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8123 (pm20) REVERT: B 79 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8209 (pm20) REVERT: C 79 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8227 (pm20) REVERT: D 79 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8206 (pm20) REVERT: I 209 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: I 217 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7469 (tmtt) REVERT: I 242 MET cc_start: 0.5164 (tpp) cc_final: 0.4743 (tpp) REVERT: J 209 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: J 217 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7363 (tmtt) REVERT: J 242 MET cc_start: 0.5440 (tpp) cc_final: 0.4541 (tpp) REVERT: K 160 ASP cc_start: 0.7952 (m-30) cc_final: 0.7259 (t70) REVERT: K 242 MET cc_start: 0.5742 (tpp) cc_final: 0.4910 (tpp) REVERT: L 77 GLN cc_start: 0.6949 (mt0) cc_final: 0.6747 (mm-40) REVERT: L 87 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8183 (mmmt) REVERT: L 209 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: L 217 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7241 (tmtt) outliers start: 52 outliers final: 25 residues processed: 262 average time/residue: 1.7124 time to fit residues: 476.8892 Evaluate side-chains 265 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 229 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain I residue 116 GLN Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain I residue 217 LYS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 236 GLN Chi-restraints excluded: chain J residue 116 GLN Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 209 GLU Chi-restraints excluded: chain J residue 217 LYS Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 236 GLN Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 236 GLN Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 209 GLU Chi-restraints excluded: chain L residue 217 LYS Chi-restraints excluded: chain L residue 225 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 120 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 1 optimal weight: 0.0670 chunk 82 optimal weight: 0.5980 chunk 138 optimal weight: 0.0770 chunk 110 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 86 optimal weight: 0.2980 chunk 109 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 81 GLN A 477 GLN B 56 GLN B 81 GLN B 477 GLN C 56 GLN C 81 GLN C 477 GLN D 56 GLN D 81 GLN D 477 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.179308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.125787 restraints weight = 13086.497| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.02 r_work: 0.3401 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12636 Z= 0.113 Angle : 0.483 5.197 17056 Z= 0.257 Chirality : 0.039 0.176 1768 Planarity : 0.003 0.027 2264 Dihedral : 4.062 33.495 1680 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.52 % Allowed : 18.91 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.23), residues: 1504 helix: 1.77 (0.17), residues: 968 sheet: 0.09 (0.92), residues: 40 loop : 0.00 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 19 HIS 0.002 0.001 HIS D 77 PHE 0.012 0.002 PHE A 84 TYR 0.020 0.001 TYR K 197 ARG 0.004 0.000 ARG D 429 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 741) hydrogen bonds : angle 4.73322 ( 2103) metal coordination : bond 0.00364 ( 16) metal coordination : angle 1.99786 ( 12) covalent geometry : bond 0.00241 (12620) covalent geometry : angle 0.48075 (17044) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 235 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8169 (pm20) REVERT: B 79 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8192 (pm20) REVERT: B 434 ARG cc_start: 0.7133 (ttm110) cc_final: 0.6913 (ttp-110) REVERT: C 79 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8213 (pm20) REVERT: D 79 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8199 (pm20) REVERT: I 116 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7312 (mp10) REVERT: I 209 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: I 217 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7328 (tmtt) REVERT: J 116 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7308 (mp10) REVERT: J 209 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: K 160 ASP cc_start: 0.7950 (m-30) cc_final: 0.7273 (t70) REVERT: K 242 MET cc_start: 0.5664 (tpp) cc_final: 0.5315 (tpp) REVERT: L 209 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: L 217 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7163 (tmtt) REVERT: L 232 ILE cc_start: 0.6819 (mp) cc_final: 0.6588 (mt) outliers start: 45 outliers final: 21 residues processed: 267 average time/residue: 1.5925 time to fit residues: 452.9498 Evaluate side-chains 260 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain I residue 116 GLN Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain I residue 217 LYS Chi-restraints excluded: chain I residue 236 GLN Chi-restraints excluded: chain J residue 116 GLN Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 209 GLU Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 236 GLN Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 236 GLN Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 209 GLU Chi-restraints excluded: chain L residue 217 LYS Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 226 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 50 optimal weight: 0.0000 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 chunk 103 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 chunk 118 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 81 GLN A 477 GLN B 56 GLN B 81 GLN B 477 GLN C 56 GLN C 81 GLN C 477 GLN D 56 GLN D 81 GLN D 477 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.178830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.125014 restraints weight = 13184.675| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.90 r_work: 0.3397 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12636 Z= 0.119 Angle : 0.488 6.895 17056 Z= 0.259 Chirality : 0.039 0.129 1768 Planarity : 0.003 0.028 2264 Dihedral : 3.966 33.152 1679 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.52 % Allowed : 19.61 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.23), residues: 1504 helix: 1.80 (0.17), residues: 968 sheet: 0.07 (0.92), residues: 40 loop : -0.03 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.003 0.001 HIS B 94 PHE 0.013 0.002 PHE A 84 TYR 0.018 0.001 TYR K 197 ARG 0.004 0.000 ARG A 429 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 741) hydrogen bonds : angle 4.70428 ( 2103) metal coordination : bond 0.00379 ( 16) metal coordination : angle 1.92733 ( 12) covalent geometry : bond 0.00256 (12620) covalent geometry : angle 0.48518 (17044) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8119 (pm20) REVERT: B 79 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8184 (pm20) REVERT: C 79 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8190 (pm20) REVERT: D 79 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8177 (pm20) REVERT: I 116 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: I 209 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: I 217 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7346 (tmtt) REVERT: J 116 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7313 (mp10) REVERT: J 160 ASP cc_start: 0.7928 (m-30) cc_final: 0.7309 (t70) REVERT: J 209 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: J 242 MET cc_start: 0.4886 (tpp) cc_final: 0.4471 (tpp) REVERT: K 160 ASP cc_start: 0.7968 (m-30) cc_final: 0.7312 (t70) REVERT: K 242 MET cc_start: 0.5648 (tpp) cc_final: 0.5319 (tpp) REVERT: L 87 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8220 (mmmt) REVERT: L 209 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: L 217 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7132 (tmtt) outliers start: 45 outliers final: 22 residues processed: 259 average time/residue: 1.6335 time to fit residues: 449.9996 Evaluate side-chains 261 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain I residue 116 GLN Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain I residue 217 LYS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 236 GLN Chi-restraints excluded: chain J residue 116 GLN Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 209 GLU Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 236 GLN Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 236 GLN Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 209 GLU Chi-restraints excluded: chain L residue 217 LYS Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 226 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 149 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 98 optimal weight: 0.0050 chunk 71 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 81 GLN A 477 GLN B 56 GLN B 81 GLN B 477 GLN C 56 GLN C 81 GLN C 477 GLN D 56 GLN D 81 GLN D 477 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.178054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.123849 restraints weight = 13094.392| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.91 r_work: 0.3382 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12636 Z= 0.130 Angle : 0.500 5.752 17056 Z= 0.265 Chirality : 0.040 0.129 1768 Planarity : 0.004 0.031 2264 Dihedral : 4.013 33.820 1679 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.44 % Allowed : 19.30 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.23), residues: 1504 helix: 1.79 (0.17), residues: 968 sheet: -0.08 (0.91), residues: 40 loop : -0.01 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 19 HIS 0.003 0.001 HIS D 491 PHE 0.014 0.002 PHE C 84 TYR 0.021 0.001 TYR K 197 ARG 0.003 0.000 ARG A 429 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 741) hydrogen bonds : angle 4.72280 ( 2103) metal coordination : bond 0.00451 ( 16) metal coordination : angle 1.95860 ( 12) covalent geometry : bond 0.00284 (12620) covalent geometry : angle 0.49728 (17044) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 227 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8108 (pm20) REVERT: B 79 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8170 (pm20) REVERT: C 79 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8164 (pm20) REVERT: D 79 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8161 (pm20) REVERT: D 445 MET cc_start: 0.6748 (tpt) cc_final: 0.6360 (tpp) REVERT: I 116 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7302 (mp10) REVERT: I 209 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: I 217 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7296 (tmtt) REVERT: J 116 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7302 (mp10) REVERT: J 160 ASP cc_start: 0.7935 (m-30) cc_final: 0.7297 (t70) REVERT: J 209 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: K 116 GLN cc_start: 0.7957 (pt0) cc_final: 0.7317 (mp10) REVERT: K 160 ASP cc_start: 0.8003 (m-30) cc_final: 0.7308 (t70) REVERT: K 242 MET cc_start: 0.5692 (tpp) cc_final: 0.5318 (tpp) REVERT: L 87 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8205 (mmmt) REVERT: L 116 GLN cc_start: 0.7996 (pt0) cc_final: 0.7395 (mp10) REVERT: L 209 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6948 (mp0) outliers start: 44 outliers final: 23 residues processed: 256 average time/residue: 2.0314 time to fit residues: 552.6783 Evaluate side-chains 259 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain I residue 116 GLN Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain I residue 217 LYS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 236 GLN Chi-restraints excluded: chain J residue 116 GLN Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 209 GLU Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 236 GLN Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 236 GLN Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 209 GLU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 147 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 81 GLN A 477 GLN B 56 GLN B 81 GLN B 477 GLN C 56 GLN C 81 GLN C 477 GLN D 56 GLN D 81 GLN D 477 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.177669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.123406 restraints weight = 13119.336| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.02 r_work: 0.3365 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 12636 Z= 0.140 Angle : 0.512 5.686 17056 Z= 0.273 Chirality : 0.040 0.138 1768 Planarity : 0.004 0.026 2264 Dihedral : 4.039 34.191 1679 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.20 % Allowed : 19.77 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.23), residues: 1504 helix: 1.77 (0.17), residues: 968 sheet: -0.21 (0.89), residues: 40 loop : 0.00 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 19 HIS 0.003 0.001 HIS B 77 PHE 0.015 0.002 PHE D 84 TYR 0.023 0.001 TYR K 197 ARG 0.004 0.000 ARG B 429 Details of bonding type rmsd hydrogen bonds : bond 0.04418 ( 741) hydrogen bonds : angle 4.78346 ( 2103) metal coordination : bond 0.00478 ( 16) metal coordination : angle 2.00219 ( 12) covalent geometry : bond 0.00310 (12620) covalent geometry : angle 0.50991 (17044) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8114 (pm20) REVERT: B 79 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8169 (pm20) REVERT: C 79 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8164 (pm20) REVERT: D 79 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8162 (pm20) REVERT: D 445 MET cc_start: 0.6736 (tpt) cc_final: 0.6309 (tpp) REVERT: I 116 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7333 (mp10) REVERT: I 209 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6928 (mp0) REVERT: I 217 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7265 (tmtt) REVERT: J 116 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7340 (mp10) REVERT: J 160 ASP cc_start: 0.7945 (m-30) cc_final: 0.7296 (t70) REVERT: J 209 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: J 217 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7289 (tmtt) REVERT: K 116 GLN cc_start: 0.7969 (pt0) cc_final: 0.7337 (mp10) REVERT: K 160 ASP cc_start: 0.8005 (m-30) cc_final: 0.7309 (t70) REVERT: K 242 MET cc_start: 0.5686 (tpp) cc_final: 0.5341 (tpp) REVERT: L 87 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8219 (mmmt) REVERT: L 116 GLN cc_start: 0.7968 (pt0) cc_final: 0.7395 (mp10) REVERT: L 209 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6938 (mp0) outliers start: 41 outliers final: 23 residues processed: 255 average time/residue: 1.6053 time to fit residues: 435.9468 Evaluate side-chains 265 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 230 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain I residue 116 GLN Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain I residue 217 LYS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 236 GLN Chi-restraints excluded: chain J residue 116 GLN Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 209 GLU Chi-restraints excluded: chain J residue 217 LYS Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 236 GLN Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 236 GLN Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 209 GLU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 135 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 87 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 81 GLN A 477 GLN B 56 GLN B 81 GLN B 477 GLN C 56 GLN C 81 GLN C 477 GLN D 56 GLN D 81 GLN D 477 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.177959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.124139 restraints weight = 13171.910| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.00 r_work: 0.3374 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 12636 Z= 0.130 Angle : 0.503 5.653 17056 Z= 0.267 Chirality : 0.040 0.133 1768 Planarity : 0.004 0.027 2264 Dihedral : 4.015 34.451 1679 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.28 % Allowed : 19.77 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.23), residues: 1504 helix: 1.77 (0.17), residues: 968 sheet: -0.24 (0.89), residues: 40 loop : 0.01 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 19 HIS 0.003 0.001 HIS D 77 PHE 0.014 0.002 PHE A 84 TYR 0.023 0.001 TYR K 197 ARG 0.003 0.000 ARG B 434 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 741) hydrogen bonds : angle 4.77451 ( 2103) metal coordination : bond 0.00462 ( 16) metal coordination : angle 2.06562 ( 12) covalent geometry : bond 0.00287 (12620) covalent geometry : angle 0.50007 (17044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14983.12 seconds wall clock time: 258 minutes 47.63 seconds (15527.63 seconds total)