Starting phenix.real_space_refine on Wed Mar 4 08:45:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ukh_26581/03_2026/7ukh_26581.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ukh_26581/03_2026/7ukh_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ukh_26581/03_2026/7ukh_26581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ukh_26581/03_2026/7ukh_26581.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ukh_26581/03_2026/7ukh_26581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ukh_26581/03_2026/7ukh_26581.map" } resolution = 2.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ARG:plan': 3, 'GLN:plan1': 3, 'GLU:plan': 2, '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: {'ARG:plan': 2, 'GLU:plan': 1} 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: B, C, D, J, K, L Time building chain proxies: 1.67, per 1000 atoms: 0.14 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: 0.88 Conformation dependent library (CDL) restraints added in 403.3 milliseconds 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: 0.33 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: 1.83 Time building geometry restraints manager: 1.12 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 9.190 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.630 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.170 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (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 ARG 0.003 0.001 ARG B 434 TYR 0.014 0.002 TYR L 126 PHE 0.018 0.002 PHE D 84 TRP 0.008 0.001 TRP D 19 HIS 0.005 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00425 (12620) covalent geometry : angle 0.60862 (17044) hydrogen bonds : bond 0.11678 ( 741) hydrogen bonds : angle 6.06790 ( 2103) metal coordination : bond 0.02291 ( 16) metal coordination : angle 2.67425 ( 12) *********************** 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 : 0.497 Fit side-chains outliers start: 23 outliers final: 10 residues processed: 258 average time/residue: 0.7474 time to fit residues: 205.0436 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 : 0.438 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.0070 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 = 0.4189 r_free = 0.4189 target = 0.178514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.124479 restraints weight = 13096.083| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.01 r_work: 0.3377 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12636 Z= 0.129 Angle : 0.511 5.141 17056 Z= 0.276 Chirality : 0.040 0.127 1768 Planarity : 0.004 0.035 2264 Dihedral : 4.335 28.487 1688 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.89 % Allowed : 17.81 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.22), residues: 1504 helix: 1.44 (0.17), residues: 968 sheet: -0.20 (0.90), residues: 40 loop : -0.03 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 162 TYR 0.010 0.001 TYR K 197 PHE 0.013 0.002 PHE A 84 TRP 0.006 0.001 TRP B 19 HIS 0.003 0.001 HIS D 77 Details of bonding type rmsd covalent geometry : bond 0.00268 (12620) covalent geometry : angle 0.50840 (17044) hydrogen bonds : bond 0.04613 ( 741) hydrogen bonds : angle 5.07254 ( 2103) metal coordination : bond 0.00415 ( 16) metal coordination : angle 2.13742 ( 12) *********************** 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 281 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 244 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 77 GLN cc_start: 0.7015 (mt0) cc_final: 0.6788 (mm-40) REVERT: I 212 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7978 (mm-30) REVERT: I 229 GLU cc_start: 0.6846 (mp0) cc_final: 0.6581 (pm20) REVERT: I 250 ASN cc_start: 0.7876 (m-40) cc_final: 0.7580 (m-40) outliers start: 37 outliers final: 17 residues processed: 262 average time/residue: 0.7707 time to fit residues: 214.4530 Evaluate side-chains 246 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 229 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 22 VAL 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 225 VAL Chi-restraints excluded: chain J residue 232 ILE 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 232 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4172 r_free = 0.4172 target = 0.176948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122319 restraints weight = 13115.959| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.89 r_work: 0.3360 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1121 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= 0.151 Angle : 0.513 5.164 17056 Z= 0.274 Chirality : 0.041 0.125 1768 Planarity : 0.004 0.029 2264 Dihedral : 4.334 31.467 1682 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.22), residues: 1504 helix: 1.56 (0.17), residues: 968 sheet: -0.30 (0.89), residues: 40 loop : -0.00 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 429 TYR 0.010 0.002 TYR D 444 PHE 0.016 0.002 PHE L 118 TRP 0.007 0.001 TRP B 19 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00327 (12620) covalent geometry : angle 0.50978 (17044) hydrogen bonds : bond 0.04848 ( 741) hydrogen bonds : angle 4.94306 ( 2103) metal coordination : bond 0.00461 ( 16) metal coordination : angle 2.18374 ( 12) *********************** 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 272 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 ARG cc_start: 0.6745 (mpt180) cc_final: 0.6537 (mpt180) REVERT: B 429 ARG cc_start: 0.6669 (mpt180) cc_final: 0.6453 (mpt180) REVERT: C 429 ARG cc_start: 0.6698 (mpt180) cc_final: 0.6491 (mpt180) REVERT: D 429 ARG cc_start: 0.6689 (mpt180) cc_final: 0.6474 (mpt180) REVERT: I 77 GLN cc_start: 0.7023 (mt0) cc_final: 0.6809 (mm-40) REVERT: I 242 MET cc_start: 0.5611 (tpp) cc_final: 0.4708 (tpp) REVERT: J 217 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7626 (tmtt) REVERT: K 108 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: L 77 GLN cc_start: 0.6987 (mt0) cc_final: 0.6684 (mm-40) REVERT: L 242 MET cc_start: 0.5706 (tpp) cc_final: 0.5362 (tpp) outliers start: 43 outliers final: 21 residues processed: 254 average time/residue: 0.7566 time to fit residues: 204.4750 Evaluate side-chains 251 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 100 ARG 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 141 ARG Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 100 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 108 GLU 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: 1.9990 chunk 139 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4171 r_free = 0.4171 target = 0.176874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.122091 restraints weight = 12991.096| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.90 r_work: 0.3356 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12636 Z= 0.157 Angle : 0.514 5.162 17056 Z= 0.276 Chirality : 0.041 0.125 1768 Planarity : 0.004 0.028 2264 Dihedral : 4.262 33.238 1680 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.20 % Allowed : 18.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.22), residues: 1504 helix: 1.59 (0.17), residues: 968 sheet: -0.45 (0.87), residues: 40 loop : -0.03 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 94 TYR 0.010 0.002 TYR A 106 PHE 0.017 0.002 PHE L 118 TRP 0.007 0.001 TRP D 19 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00343 (12620) covalent geometry : angle 0.51128 (17044) hydrogen bonds : bond 0.04798 ( 741) hydrogen bonds : angle 4.90706 ( 2103) metal coordination : bond 0.00435 ( 16) metal coordination : angle 2.15828 ( 12) *********************** 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 267 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 ARG cc_start: 0.6695 (mpt180) cc_final: 0.6280 (mtt-85) REVERT: B 429 ARG cc_start: 0.6778 (mpt180) cc_final: 0.6261 (mtt-85) REVERT: C 429 ARG cc_start: 0.6743 (mpt180) cc_final: 0.6248 (mtt-85) REVERT: D 429 ARG cc_start: 0.6734 (mpt180) cc_final: 0.6249 (mtt-85) REVERT: I 217 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7526 (tmtt) REVERT: I 242 MET cc_start: 0.5614 (tpp) cc_final: 0.5043 (tpp) REVERT: J 217 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7555 (tmtt) REVERT: K 108 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: K 160 ASP cc_start: 0.8058 (m-30) cc_final: 0.7344 (t70) REVERT: L 77 GLN cc_start: 0.6986 (mt0) cc_final: 0.6697 (mm-40) outliers start: 41 outliers final: 26 residues processed: 247 average time/residue: 0.8019 time to fit residues: 209.6992 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 : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 100 ARG 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 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 100 ARG 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 217 LYS 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 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 184 LEU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 226 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 105 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4171 r_free = 0.4171 target = 0.176873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.122217 restraints weight = 13159.460| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.91 r_work: 0.3356 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12636 Z= 0.153 Angle : 0.515 5.198 17056 Z= 0.275 Chirality : 0.040 0.123 1768 Planarity : 0.004 0.027 2264 Dihedral : 4.258 34.241 1680 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.06 % Allowed : 18.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.22), residues: 1504 helix: 1.63 (0.17), residues: 968 sheet: -0.47 (0.86), residues: 40 loop : -0.06 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 429 TYR 0.010 0.002 TYR B 106 PHE 0.017 0.002 PHE L 118 TRP 0.006 0.001 TRP C 19 HIS 0.004 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00339 (12620) covalent geometry : angle 0.51153 (17044) hydrogen bonds : bond 0.04712 ( 741) hydrogen bonds : angle 4.87538 ( 2103) metal coordination : bond 0.00474 ( 16) metal coordination : angle 2.16490 ( 12) *********************** 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 281 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 229 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8229 (pm20) REVERT: A 429 ARG cc_start: 0.6694 (mpt180) cc_final: 0.6307 (mmt180) REVERT: B 429 ARG cc_start: 0.6798 (mpt180) cc_final: 0.6428 (mtt-85) REVERT: C 429 ARG cc_start: 0.6761 (mpt180) cc_final: 0.6380 (mtt-85) REVERT: D 429 ARG cc_start: 0.6788 (mpt180) cc_final: 0.6395 (mtt-85) REVERT: I 217 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7502 (tmtt) REVERT: I 242 MET cc_start: 0.5516 (tpp) cc_final: 0.4841 (tpp) REVERT: J 217 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7476 (tmtt) REVERT: K 108 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: K 160 ASP cc_start: 0.8059 (m-30) cc_final: 0.7344 (t70) REVERT: L 77 GLN cc_start: 0.7001 (mt0) cc_final: 0.6794 (mm-40) outliers start: 52 outliers final: 28 residues processed: 254 average time/residue: 0.7596 time to fit residues: 205.2790 Evaluate side-chains 257 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 141 ARG Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 100 ARG 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 100 ARG 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 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 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 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 184 LEU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 226 VAL Chi-restraints excluded: chain L residue 236 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 8 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 62 optimal weight: 0.0470 chunk 54 optimal weight: 1.9990 chunk 140 optimal weight: 0.1980 chunk 68 optimal weight: 0.6980 chunk 22 optimal weight: 0.0570 chunk 61 optimal weight: 0.6980 chunk 60 optimal weight: 0.0970 overall best weight: 0.2194 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.180636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127305 restraints weight = 13118.878| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.02 r_work: 0.3422 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12636 Z= 0.102 Angle : 0.457 5.106 17056 Z= 0.242 Chirality : 0.038 0.129 1768 Planarity : 0.003 0.023 2264 Dihedral : 4.024 32.314 1680 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.19 % Allowed : 20.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.22), residues: 1504 helix: 1.75 (0.17), residues: 968 sheet: 0.36 (0.93), residues: 40 loop : -0.02 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 434 TYR 0.008 0.001 TYR K 197 PHE 0.009 0.001 PHE A 84 TRP 0.002 0.001 TRP A 19 HIS 0.002 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00209 (12620) covalent geometry : angle 0.45355 (17044) hydrogen bonds : bond 0.03720 ( 741) hydrogen bonds : angle 4.69750 ( 2103) metal coordination : bond 0.00325 ( 16) metal coordination : angle 2.04819 ( 12) *********************** 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 275 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 247 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8201 (pm20) REVERT: A 429 ARG cc_start: 0.6743 (mpt180) cc_final: 0.6372 (mtt-85) REVERT: B 79 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8237 (pm20) REVERT: C 79 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8228 (pm20) REVERT: D 79 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8216 (pm20) REVERT: I 76 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6844 (mp0) REVERT: J 160 ASP cc_start: 0.7900 (m-30) cc_final: 0.7278 (t70) REVERT: K 160 ASP cc_start: 0.7961 (m-30) cc_final: 0.7262 (t70) REVERT: K 242 MET cc_start: 0.5622 (tpp) cc_final: 0.5314 (tpp) REVERT: L 116 GLN cc_start: 0.7950 (pt0) cc_final: 0.7727 (pt0) outliers start: 28 outliers final: 12 residues processed: 264 average time/residue: 0.7821 time to fit residues: 219.1280 Evaluate side-chains 249 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 233 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain I residue 184 LEU 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 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 Chi-restraints excluded: chain L residue 236 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 140 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 41 optimal weight: 0.0060 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.0270 chunk 123 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 overall best weight: 0.4454 ------------------------------------------------------------------------------- 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 = 0.179468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.125831 restraints weight = 13051.879| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.00 r_work: 0.3399 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12636 Z= 0.114 Angle : 0.472 6.133 17056 Z= 0.250 Chirality : 0.039 0.127 1768 Planarity : 0.003 0.023 2264 Dihedral : 3.988 31.880 1680 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.58 % Allowed : 19.53 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.22), residues: 1504 helix: 1.84 (0.17), residues: 968 sheet: 0.20 (0.92), residues: 40 loop : -0.04 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 429 TYR 0.007 0.001 TYR C 444 PHE 0.012 0.002 PHE A 84 TRP 0.004 0.001 TRP D 19 HIS 0.003 0.001 HIS D 77 Details of bonding type rmsd covalent geometry : bond 0.00242 (12620) covalent geometry : angle 0.46926 (17044) hydrogen bonds : bond 0.03971 ( 741) hydrogen bonds : angle 4.65432 ( 2103) metal coordination : bond 0.00391 ( 16) metal coordination : angle 1.80730 ( 12) *********************** 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 267 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8178 (pm20) REVERT: B 79 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: C 79 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8202 (pm20) REVERT: D 79 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8181 (pm20) REVERT: I 76 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6896 (mp0) REVERT: J 160 ASP cc_start: 0.7906 (m-30) cc_final: 0.7289 (t70) REVERT: K 160 ASP cc_start: 0.8014 (m-30) cc_final: 0.7307 (t70) REVERT: K 242 MET cc_start: 0.5575 (tpp) cc_final: 0.5149 (tpp) REVERT: L 116 GLN cc_start: 0.7919 (pt0) cc_final: 0.7673 (pt0) outliers start: 33 outliers final: 17 residues processed: 253 average time/residue: 0.7615 time to fit residues: 204.7414 Evaluate side-chains 255 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 234 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU 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 141 ARG 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 225 VAL Chi-restraints excluded: chain I residue 236 GLN Chi-restraints excluded: chain J residue 184 LEU 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 Chi-restraints excluded: chain L residue 236 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 138 optimal weight: 0.1980 chunk 64 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4171 r_free = 0.4171 target = 0.176817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122354 restraints weight = 13056.188| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.89 r_work: 0.3357 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12636 Z= 0.160 Angle : 0.528 7.692 17056 Z= 0.280 Chirality : 0.041 0.125 1768 Planarity : 0.004 0.031 2264 Dihedral : 4.176 34.168 1680 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.05 % Allowed : 19.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.22), residues: 1504 helix: 1.76 (0.17), residues: 968 sheet: -0.46 (0.87), residues: 40 loop : -0.04 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 429 TYR 0.011 0.002 TYR C 444 PHE 0.018 0.002 PHE D 11 TRP 0.006 0.001 TRP B 19 HIS 0.004 0.001 HIS A 491 Details of bonding type rmsd covalent geometry : bond 0.00355 (12620) covalent geometry : angle 0.52509 (17044) hydrogen bonds : bond 0.04742 ( 741) hydrogen bonds : angle 4.80924 ( 2103) metal coordination : bond 0.00499 ( 16) metal coordination : angle 1.99606 ( 12) *********************** 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 264 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8123 (pm20) REVERT: B 79 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8217 (pm20) REVERT: C 79 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: D 79 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8170 (pm20) REVERT: J 116 GLN cc_start: 0.8006 (pt0) cc_final: 0.7424 (mp10) REVERT: J 217 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7385 (tmtt) REVERT: K 116 GLN cc_start: 0.8006 (pt0) cc_final: 0.7433 (mp10) REVERT: K 160 ASP cc_start: 0.8039 (m-30) cc_final: 0.7338 (t70) REVERT: K 242 MET cc_start: 0.5718 (tpp) cc_final: 0.4633 (tpp) REVERT: L 87 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8238 (mmmt) outliers start: 39 outliers final: 19 residues processed: 246 average time/residue: 0.7901 time to fit residues: 206.2230 Evaluate side-chains 245 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 141 ARG Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 79 GLU 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 184 LEU 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 217 LYS Chi-restraints excluded: chain J residue 225 VAL 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 225 VAL Chi-restraints excluded: chain L residue 236 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 89 optimal weight: 0.9980 chunk 95 optimal weight: 0.0370 chunk 137 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 overall best weight: 0.7458 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.177741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123463 restraints weight = 13041.835| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.06 r_work: 0.3358 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12636 Z= 0.137 Angle : 0.508 7.968 17056 Z= 0.268 Chirality : 0.040 0.126 1768 Planarity : 0.004 0.023 2264 Dihedral : 4.146 34.693 1680 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.58 % Allowed : 20.23 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.22), residues: 1504 helix: 1.76 (0.17), residues: 968 sheet: -0.41 (0.88), residues: 40 loop : -0.04 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 429 TYR 0.009 0.001 TYR C 444 PHE 0.015 0.002 PHE B 92 TRP 0.006 0.001 TRP D 19 HIS 0.003 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00300 (12620) covalent geometry : angle 0.50596 (17044) hydrogen bonds : bond 0.04379 ( 741) hydrogen bonds : angle 4.76568 ( 2103) metal coordination : bond 0.00465 ( 16) metal coordination : angle 1.95894 ( 12) *********************** 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 263 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 230 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8132 (pm20) REVERT: B 79 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8203 (pm20) REVERT: C 79 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8190 (pm20) REVERT: D 79 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: I 217 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7303 (tmtt) REVERT: J 116 GLN cc_start: 0.7993 (pt0) cc_final: 0.7413 (mp10) REVERT: K 116 GLN cc_start: 0.8017 (pt0) cc_final: 0.7421 (mp10) REVERT: K 160 ASP cc_start: 0.8025 (m-30) cc_final: 0.7321 (t70) REVERT: K 242 MET cc_start: 0.5631 (tpp) cc_final: 0.4730 (tpp) REVERT: L 87 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8212 (mmmt) REVERT: L 116 GLN cc_start: 0.7906 (pt0) cc_final: 0.7258 (mp10) outliers start: 33 outliers final: 20 residues processed: 251 average time/residue: 0.7666 time to fit residues: 204.4510 Evaluate side-chains 255 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 141 ARG Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 79 GLU 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 184 LEU 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 184 LEU 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 225 VAL Chi-restraints excluded: chain L residue 236 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 96 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 98 optimal weight: 0.0980 chunk 151 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 chunk 143 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 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 = 0.178074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124069 restraints weight = 13101.373| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.02 r_work: 0.3369 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12636 Z= 0.128 Angle : 0.498 7.747 17056 Z= 0.263 Chirality : 0.040 0.126 1768 Planarity : 0.003 0.023 2264 Dihedral : 4.104 34.727 1680 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.58 % Allowed : 20.31 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.22), residues: 1504 helix: 1.78 (0.17), residues: 968 sheet: -0.25 (0.89), residues: 40 loop : -0.00 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 429 TYR 0.008 0.001 TYR C 444 PHE 0.014 0.002 PHE A 84 TRP 0.005 0.001 TRP A 19 HIS 0.003 0.001 HIS D 77 Details of bonding type rmsd covalent geometry : bond 0.00279 (12620) covalent geometry : angle 0.49528 (17044) hydrogen bonds : bond 0.04246 ( 741) hydrogen bonds : angle 4.71497 ( 2103) metal coordination : bond 0.00512 ( 16) metal coordination : angle 1.96220 ( 12) ********************** 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 264 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8133 (pm20) REVERT: B 79 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8193 (pm20) REVERT: C 79 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: D 79 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8185 (pm20) REVERT: I 116 GLN cc_start: 0.7977 (pt0) cc_final: 0.7327 (mp10) REVERT: J 116 GLN cc_start: 0.7972 (pt0) cc_final: 0.7405 (mp10) REVERT: K 116 GLN cc_start: 0.7910 (pt0) cc_final: 0.7321 (mp10) REVERT: K 160 ASP cc_start: 0.8021 (m-30) cc_final: 0.7324 (t70) REVERT: K 242 MET cc_start: 0.5608 (tpp) cc_final: 0.5010 (tpp) REVERT: L 87 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8235 (mmmt) REVERT: L 116 GLN cc_start: 0.7859 (pt0) cc_final: 0.7276 (mp10) outliers start: 33 outliers final: 20 residues processed: 251 average time/residue: 0.7775 time to fit residues: 206.8933 Evaluate side-chains 255 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 230 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 141 ARG Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 79 GLU 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 184 LEU 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 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 225 VAL Chi-restraints excluded: chain L residue 236 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 39 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 108 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.177345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123104 restraints weight = 13075.794| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.89 r_work: 0.3370 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12636 Z= 0.144 Angle : 0.513 7.418 17056 Z= 0.272 Chirality : 0.040 0.125 1768 Planarity : 0.004 0.028 2264 Dihedral : 4.153 35.634 1680 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.27 % Allowed : 20.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.22), residues: 1504 helix: 1.74 (0.17), residues: 968 sheet: -0.45 (0.87), residues: 40 loop : 0.03 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 434 TYR 0.010 0.001 TYR C 444 PHE 0.015 0.002 PHE K 118 TRP 0.006 0.001 TRP D 19 HIS 0.003 0.001 HIS D 77 Details of bonding type rmsd covalent geometry : bond 0.00317 (12620) covalent geometry : angle 0.51010 (17044) hydrogen bonds : bond 0.04489 ( 741) hydrogen bonds : angle 4.74942 ( 2103) metal coordination : bond 0.00494 ( 16) metal coordination : angle 1.94255 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6792.01 seconds wall clock time: 115 minutes 39.82 seconds (6939.82 seconds total)