Starting phenix.real_space_refine on Wed Sep 17 10:45:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vvh_43559/09_2025/8vvh_43559.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vvh_43559/09_2025/8vvh_43559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vvh_43559/09_2025/8vvh_43559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vvh_43559/09_2025/8vvh_43559.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vvh_43559/09_2025/8vvh_43559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vvh_43559/09_2025/8vvh_43559.map" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1632 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 4368 2.51 5 N 1180 2.21 5 O 1302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6877 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2684 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 17, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 5, 'HIS:plan': 2, 'GLU:plan': 11, 'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 134 Chain: "B" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2624 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 13, 'TRANS': 340} Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 10, 'GLU:plan': 12, 'HIS:plan': 4, 'ARG:plan': 3, 'PHE:plan': 1, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 140 Chain: "H" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 833 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 108} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "L" Number of atoms: 736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 726 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 101} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 48 Conformer: "B" Number of residues, atoms: 108, 726 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 101} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 48 bond proxies already assigned to first conformer: 728 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS L 8 " occ=0.82 ... (18 atoms not shown) pdb=" NE2BHIS L 8 " occ=0.18 Time building chain proxies: 1.92, per 1000 atoms: 0.28 Number of scatterers: 6877 At special positions: 0 Unit cell: (109.568, 123.264, 83.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 1302 8.00 N 1180 7.00 C 4368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 393.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1754 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 12 sheets defined 28.3% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 36 through 51 removed outlier: 3.507A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.627A pdb=" N SER A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 115 removed outlier: 3.695A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.561A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.925A pdb=" N GLN A 147 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.924A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 224 through 238 removed outlier: 4.471A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 4.068A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 removed outlier: 3.700A pdb=" N SER A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 4.059A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 119 Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.587A pdb=" N ALA B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 3.761A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 223 removed outlier: 4.015A pdb=" N ILE B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 223 " --> pdb=" O GLN B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 removed outlier: 3.857A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.908A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 312 Processing helix chain 'B' and resid 333 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 removed outlier: 6.357A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 6.854A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER A 168 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.095A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN A 357 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 69 through 72 removed outlier: 6.328A pdb=" N VAL B 39 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ALA B 100 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE B 40 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N PHE B 99 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY B 128 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ASP B 101 " --> pdb=" O GLY B 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.308A pdb=" N SER B 170 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N TYR B 231 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 228 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 280 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 362 " --> pdb=" O TRP B 379 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 343 through 344 removed outlier: 3.951A pdb=" N PHE B 344 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 20 through 21 removed outlier: 3.718A pdb=" N LEU H 20 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 51 through 52 Processing sheet with id=AA9, first strand: chain 'H' and resid 39 through 40 Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AB2, first strand: chain 'L' and resid 46 through 50 removed outlier: 6.631A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER L 93 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL L 100 " --> pdb=" O SER L 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 46 through 50 removed outlier: 6.631A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.95 Time building geometry restraints manager: 0.53 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: 2263 1.34 - 1.46: 1659 1.46 - 1.58: 3053 1.58 - 1.71: 0 1.71 - 1.83: 45 Bond restraints: 7020 Sorted by residual: bond pdb=" CA ILE L 29 " pdb=" CB ILE L 29 " ideal model delta sigma weight residual 1.527 1.547 -0.020 1.31e-02 5.83e+03 2.43e+00 bond pdb=" CA VAL B 258 " pdb=" CB VAL B 258 " ideal model delta sigma weight residual 1.547 1.536 0.011 1.10e-02 8.26e+03 1.02e+00 bond pdb=" CB GLU L 51 " pdb=" CG GLU L 51 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.36e-01 bond pdb=" CB ASP B 138 " pdb=" CG ASP B 138 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 6.89e-01 bond pdb=" CD GLU L 51 " pdb=" OE1 GLU L 51 " ideal model delta sigma weight residual 1.249 1.234 0.015 1.90e-02 2.77e+03 6.45e-01 ... (remaining 7015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 9347 1.66 - 3.32: 197 3.32 - 4.98: 31 4.98 - 6.64: 10 6.64 - 8.30: 6 Bond angle restraints: 9591 Sorted by residual: angle pdb=" N VAL B 376 " pdb=" CA VAL B 376 " pdb=" C VAL B 376 " ideal model delta sigma weight residual 113.71 110.66 3.05 9.50e-01 1.11e+00 1.03e+01 angle pdb=" N GLY H 56 " pdb=" CA GLY H 56 " pdb=" C GLY H 56 " ideal model delta sigma weight residual 113.18 120.59 -7.41 2.37e+00 1.78e-01 9.78e+00 angle pdb=" CA ILE L 29 " pdb=" CB ILE L 29 " pdb=" CG1 ILE L 29 " ideal model delta sigma weight residual 110.40 115.64 -5.24 1.70e+00 3.46e-01 9.51e+00 angle pdb=" C GLU A 213 " pdb=" N LEU A 214 " pdb=" CA LEU A 214 " ideal model delta sigma weight residual 121.54 116.32 5.22 1.91e+00 2.74e-01 7.48e+00 angle pdb=" C THR H 23 " pdb=" N VAL H 24 " pdb=" CA VAL H 24 " ideal model delta sigma weight residual 121.97 126.79 -4.82 1.80e+00 3.09e-01 7.16e+00 ... (remaining 9586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 3545 17.51 - 35.02: 459 35.02 - 52.53: 126 52.53 - 70.04: 18 70.04 - 87.55: 7 Dihedral angle restraints: 4155 sinusoidal: 1429 harmonic: 2726 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual -86.00 -133.41 47.41 1 1.00e+01 1.00e-02 3.10e+01 dihedral pdb=" CA GLU A 215 " pdb=" C GLU A 215 " pdb=" N ALA A 216 " pdb=" CA ALA A 216 " ideal model delta harmonic sigma weight residual 180.00 -158.63 -21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 91 " pdb=" CB CYS L 91 " ideal model delta sinusoidal sigma weight residual 93.00 58.31 34.69 1 1.00e+01 1.00e-02 1.71e+01 ... (remaining 4152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 825 0.042 - 0.084: 216 0.084 - 0.126: 79 0.126 - 0.169: 7 0.169 - 0.211: 3 Chirality restraints: 1130 Sorted by residual: chirality pdb=" CB ILE B 35 " pdb=" CA ILE B 35 " pdb=" CG1 ILE B 35 " pdb=" CG2 ILE B 35 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA GLU L 51 " pdb=" N GLU L 51 " pdb=" C GLU L 51 " pdb=" CB GLU L 51 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CB ILE B 190 " pdb=" CA ILE B 190 " pdb=" CG1 ILE B 190 " pdb=" CG2 ILE B 190 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.08e-01 ... (remaining 1127 not shown) Planarity restraints: 1230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 289 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO B 290 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 290 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 290 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 318 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO A 319 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 319 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 319 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 50 " -0.008 2.00e-02 2.50e+03 1.05e-02 2.21e+00 pdb=" CG TYR L 50 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR L 50 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR L 50 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR L 50 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR L 50 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR L 50 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR L 50 " 0.001 2.00e-02 2.50e+03 ... (remaining 1227 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 961 2.76 - 3.29: 6587 3.29 - 3.83: 10529 3.83 - 4.36: 10885 4.36 - 4.90: 19889 Nonbonded interactions: 48851 Sorted by model distance: nonbonded pdb=" NH1 ARG L 24 " pdb=" O SER L 26 " model vdw 2.220 3.120 nonbonded pdb=" OG SER B 149 " pdb=" OE1 GLN B 152 " model vdw 2.240 3.040 nonbonded pdb=" O MET B 89 " pdb=" OG SER B 319 " model vdw 2.253 3.040 nonbonded pdb=" ND2 ASN L 32 " pdb=" O TYR L 94 " model vdw 2.283 3.120 nonbonded pdb=" NH2 ARG L 40 " pdb=" O GLU L 84 " model vdw 2.291 3.120 ... (remaining 48846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.18 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 : 0.002 0.029 7024 Z= 0.115 Angle : 0.614 8.302 9599 Z= 0.313 Chirality : 0.044 0.211 1130 Planarity : 0.004 0.054 1230 Dihedral : 17.029 87.552 2389 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.09 % Favored : 92.70 % Rotamer: Outliers : 0.88 % Allowed : 35.98 % Favored : 63.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -1.64 (0.27), residues: 934 helix: 1.11 (0.33), residues: 249 sheet: -1.06 (0.36), residues: 222 loop : -2.44 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.026 0.001 TYR L 50 PHE 0.008 0.001 PHE A 197 TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 7020) covalent geometry : angle 0.61386 ( 9591) SS BOND : bond 0.00310 ( 4) SS BOND : angle 1.02882 ( 8) hydrogen bonds : bond 0.16224 ( 244) hydrogen bonds : angle 5.97565 ( 702) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 0.272 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 147 average time/residue: 0.0691 time to fit residues: 14.1908 Evaluate side-chains 143 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain L residue 51 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.0370 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.172221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.141077 restraints weight = 34741.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143771 restraints weight = 23689.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.140533 restraints weight = 10296.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.141464 restraints weight = 11563.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.142451 restraints weight = 7515.271| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7024 Z= 0.128 Angle : 0.590 13.042 9599 Z= 0.300 Chirality : 0.043 0.161 1130 Planarity : 0.004 0.056 1230 Dihedral : 4.325 34.597 1009 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.52 % Favored : 92.27 % Rotamer: Outliers : 6.61 % Allowed : 30.25 % Favored : 63.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -1.58 (0.27), residues: 934 helix: 1.00 (0.32), residues: 254 sheet: -0.83 (0.37), residues: 213 loop : -2.43 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 24 TYR 0.019 0.001 TYR L 50 PHE 0.012 0.001 PHE A 152 TRP 0.008 0.001 TRP H 34 HIS 0.002 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7020) covalent geometry : angle 0.58971 ( 9591) SS BOND : bond 0.00260 ( 4) SS BOND : angle 0.73567 ( 8) hydrogen bonds : bond 0.04037 ( 244) hydrogen bonds : angle 4.84768 ( 702) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 150 time to evaluate : 0.283 Fit side-chains REVERT: A 322 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8465 (ttmm) outliers start: 45 outliers final: 23 residues processed: 179 average time/residue: 0.0710 time to fit residues: 17.7181 Evaluate side-chains 163 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 chunk 56 optimal weight: 0.8980 chunk 20 optimal weight: 0.0980 chunk 27 optimal weight: 0.0010 chunk 30 optimal weight: 0.0060 chunk 82 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 overall best weight: 0.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN L 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.175867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.140781 restraints weight = 29106.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.144417 restraints weight = 27366.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.146911 restraints weight = 11918.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.147099 restraints weight = 9642.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.147906 restraints weight = 7581.490| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3780 r_free = 0.3780 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3780 r_free = 0.3780 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7024 Z= 0.103 Angle : 0.583 13.913 9599 Z= 0.291 Chirality : 0.043 0.157 1130 Planarity : 0.004 0.052 1230 Dihedral : 3.768 20.608 1002 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.23 % Favored : 93.56 % Rotamer: Outliers : 5.58 % Allowed : 29.96 % Favored : 64.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -1.46 (0.27), residues: 934 helix: 1.13 (0.33), residues: 256 sheet: -0.69 (0.38), residues: 213 loop : -2.41 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 24 TYR 0.012 0.001 TYR L 50 PHE 0.011 0.001 PHE B 241 TRP 0.005 0.001 TRP B 285 HIS 0.001 0.000 HIS A 371 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 7020) covalent geometry : angle 0.58227 ( 9591) SS BOND : bond 0.00933 ( 4) SS BOND : angle 1.15364 ( 8) hydrogen bonds : bond 0.03241 ( 244) hydrogen bonds : angle 4.55205 ( 702) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.282 Fit side-chains REVERT: A 132 SER cc_start: 0.8882 (OUTLIER) cc_final: 0.8499 (t) REVERT: A 322 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8224 (tttt) REVERT: B 239 TYR cc_start: 0.7049 (t80) cc_final: 0.6815 (t80) REVERT: H 44 LYS cc_start: 0.8651 (mtmm) cc_final: 0.8189 (mptt) REVERT: H 48 TRP cc_start: 0.8887 (t60) cc_final: 0.8538 (t60) outliers start: 38 outliers final: 20 residues processed: 167 average time/residue: 0.0760 time to fit residues: 17.4736 Evaluate side-chains 164 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 2 optimal weight: 0.0970 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 331 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.173099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.142485 restraints weight = 34328.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.144895 restraints weight = 23087.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.141754 restraints weight = 10140.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.142731 restraints weight = 11405.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.143519 restraints weight = 7321.416| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7024 Z= 0.118 Angle : 0.584 14.006 9599 Z= 0.293 Chirality : 0.043 0.162 1130 Planarity : 0.004 0.053 1230 Dihedral : 3.794 21.188 1002 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.09 % Favored : 92.80 % Rotamer: Outliers : 8.08 % Allowed : 27.46 % Favored : 64.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -1.43 (0.27), residues: 934 helix: 1.21 (0.33), residues: 257 sheet: -0.75 (0.37), residues: 220 loop : -2.42 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.014 0.001 TYR L 50 PHE 0.014 0.001 PHE A 152 TRP 0.006 0.001 TRP H 35 HIS 0.002 0.000 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7020) covalent geometry : angle 0.58420 ( 9591) SS BOND : bond 0.00256 ( 4) SS BOND : angle 0.83667 ( 8) hydrogen bonds : bond 0.03435 ( 244) hydrogen bonds : angle 4.48556 ( 702) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 145 time to evaluate : 0.210 Fit side-chains REVERT: A 322 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8534 (ttmm) REVERT: B 192 ASN cc_start: 0.8112 (m-40) cc_final: 0.7909 (m-40) REVERT: B 371 ARG cc_start: 0.7969 (mmm-85) cc_final: 0.7673 (mmt90) REVERT: H 44 LYS cc_start: 0.8690 (mtmm) cc_final: 0.8201 (mptt) outliers start: 55 outliers final: 38 residues processed: 182 average time/residue: 0.0744 time to fit residues: 18.6522 Evaluate side-chains 180 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 0.0000 chunk 68 optimal weight: 0.0470 chunk 79 optimal weight: 0.0770 chunk 22 optimal weight: 0.3980 chunk 87 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.175273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.143233 restraints weight = 34701.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.146245 restraints weight = 24959.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.147404 restraints weight = 9766.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.148326 restraints weight = 8410.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.148695 restraints weight = 6402.476| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7024 Z= 0.099 Angle : 0.588 14.971 9599 Z= 0.291 Chirality : 0.043 0.165 1130 Planarity : 0.004 0.052 1230 Dihedral : 3.725 20.487 1002 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.02 % Favored : 93.88 % Rotamer: Outliers : 6.61 % Allowed : 29.66 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -1.34 (0.27), residues: 934 helix: 1.26 (0.33), residues: 257 sheet: -0.56 (0.38), residues: 216 loop : -2.42 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.015 0.001 TYR B 239 PHE 0.009 0.001 PHE B 241 TRP 0.005 0.001 TRP B 285 HIS 0.001 0.000 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 7020) covalent geometry : angle 0.58605 ( 9591) SS BOND : bond 0.00356 ( 4) SS BOND : angle 1.55864 ( 8) hydrogen bonds : bond 0.03109 ( 244) hydrogen bonds : angle 4.39168 ( 702) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 0.298 Fit side-chains REVERT: A 322 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8561 (ttmm) REVERT: B 192 ASN cc_start: 0.8104 (m-40) cc_final: 0.7809 (m-40) REVERT: B 371 ARG cc_start: 0.7894 (mmm-85) cc_final: 0.7560 (mmt90) REVERT: H 44 LYS cc_start: 0.8658 (mtmm) cc_final: 0.8187 (mptt) REVERT: L 24 ARG cc_start: 0.8104 (ttm-80) cc_final: 0.7793 (ttm-80) outliers start: 45 outliers final: 33 residues processed: 169 average time/residue: 0.0773 time to fit residues: 18.1089 Evaluate side-chains 169 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain L residue 1 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 51 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 86 optimal weight: 0.0470 chunk 48 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 0.0470 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.175141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.139636 restraints weight = 21043.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143901 restraints weight = 23039.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.144977 restraints weight = 10475.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.145536 restraints weight = 8436.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.146244 restraints weight = 6994.616| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7024 Z= 0.101 Angle : 0.600 15.059 9599 Z= 0.291 Chirality : 0.043 0.176 1130 Planarity : 0.004 0.052 1230 Dihedral : 3.683 20.209 1002 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.55 % Favored : 93.34 % Rotamer: Outliers : 6.90 % Allowed : 29.66 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -1.34 (0.27), residues: 934 helix: 1.28 (0.33), residues: 257 sheet: -0.63 (0.37), residues: 222 loop : -2.42 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.015 0.001 TYR L 50 PHE 0.014 0.001 PHE A 152 TRP 0.005 0.001 TRP H 35 HIS 0.001 0.000 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 7020) covalent geometry : angle 0.59918 ( 9591) SS BOND : bond 0.00330 ( 4) SS BOND : angle 1.01462 ( 8) hydrogen bonds : bond 0.03064 ( 244) hydrogen bonds : angle 4.34513 ( 702) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 0.275 Fit side-chains REVERT: A 322 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8548 (ttmm) REVERT: B 192 ASN cc_start: 0.8063 (m-40) cc_final: 0.7752 (m-40) REVERT: B 257 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7329 (mt) REVERT: B 371 ARG cc_start: 0.7897 (mmm-85) cc_final: 0.7534 (mmt90) REVERT: H 44 LYS cc_start: 0.8651 (mtmm) cc_final: 0.8177 (mptt) REVERT: L 24 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7779 (ttm-80) outliers start: 47 outliers final: 39 residues processed: 170 average time/residue: 0.0698 time to fit residues: 16.2975 Evaluate side-chains 179 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain L residue 1 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 0.0670 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.172694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.141132 restraints weight = 36538.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.144508 restraints weight = 24635.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.143923 restraints weight = 9422.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.145084 restraints weight = 8398.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.145889 restraints weight = 6340.249| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7024 Z= 0.126 Angle : 0.605 14.427 9599 Z= 0.300 Chirality : 0.043 0.170 1130 Planarity : 0.004 0.052 1230 Dihedral : 3.824 21.119 1002 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.95 % Favored : 91.94 % Rotamer: Outliers : 7.49 % Allowed : 30.10 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -1.43 (0.27), residues: 934 helix: 1.19 (0.33), residues: 257 sheet: -0.81 (0.37), residues: 227 loop : -2.40 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.018 0.001 TYR B 356 PHE 0.018 0.001 PHE B 241 TRP 0.006 0.001 TRP H 34 HIS 0.002 0.000 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7020) covalent geometry : angle 0.60510 ( 9591) SS BOND : bond 0.00408 ( 4) SS BOND : angle 0.91953 ( 8) hydrogen bonds : bond 0.03466 ( 244) hydrogen bonds : angle 4.42623 ( 702) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 140 time to evaluate : 0.324 Fit side-chains REVERT: A 132 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8659 (t) REVERT: A 322 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8573 (ttmm) REVERT: B 371 ARG cc_start: 0.7935 (mmm-85) cc_final: 0.7603 (mmt90) REVERT: H 44 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8171 (mptt) REVERT: L 24 ARG cc_start: 0.8136 (ttm-80) cc_final: 0.7802 (ttm-80) outliers start: 51 outliers final: 40 residues processed: 172 average time/residue: 0.0803 time to fit residues: 19.1309 Evaluate side-chains 181 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain L residue 1 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 31 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 0.0970 chunk 42 optimal weight: 0.1980 chunk 51 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 87 optimal weight: 0.0000 overall best weight: 0.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.175089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.144793 restraints weight = 33347.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.145043 restraints weight = 22410.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.142737 restraints weight = 11040.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.143933 restraints weight = 10923.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.144509 restraints weight = 7672.513| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7024 Z= 0.104 Angle : 0.636 14.100 9599 Z= 0.308 Chirality : 0.043 0.184 1130 Planarity : 0.004 0.052 1230 Dihedral : 3.774 20.036 1002 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.55 % Favored : 93.34 % Rotamer: Outliers : 6.17 % Allowed : 31.57 % Favored : 62.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -1.35 (0.27), residues: 934 helix: 1.19 (0.33), residues: 258 sheet: -0.62 (0.37), residues: 222 loop : -2.37 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.016 0.001 TYR B 239 PHE 0.029 0.001 PHE A 152 TRP 0.005 0.001 TRP A 381 HIS 0.001 0.000 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 7020) covalent geometry : angle 0.63529 ( 9591) SS BOND : bond 0.00754 ( 4) SS BOND : angle 1.44131 ( 8) hydrogen bonds : bond 0.03089 ( 244) hydrogen bonds : angle 4.33691 ( 702) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 0.303 Fit side-chains REVERT: A 132 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8671 (t) REVERT: A 322 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8542 (ttmm) REVERT: B 273 PHE cc_start: 0.7181 (m-80) cc_final: 0.6921 (m-80) REVERT: B 371 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.7596 (mmt90) REVERT: H 44 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8163 (mptt) REVERT: H 60 TYR cc_start: 0.9265 (m-80) cc_final: 0.8843 (m-80) REVERT: L 24 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7698 (ttm-80) outliers start: 42 outliers final: 34 residues processed: 162 average time/residue: 0.0809 time to fit residues: 18.0246 Evaluate side-chains 171 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain L residue 1 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 57 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.168816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.138455 restraints weight = 34352.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.141070 restraints weight = 25152.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.140687 restraints weight = 10194.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.141688 restraints weight = 8947.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.142516 restraints weight = 6667.333| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7024 Z= 0.183 Angle : 0.688 13.319 9599 Z= 0.342 Chirality : 0.045 0.168 1130 Planarity : 0.004 0.053 1230 Dihedral : 4.160 21.841 1002 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.67 % Favored : 90.23 % Rotamer: Outliers : 6.90 % Allowed : 31.42 % Favored : 61.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -1.50 (0.27), residues: 934 helix: 1.10 (0.32), residues: 255 sheet: -0.86 (0.37), residues: 220 loop : -2.38 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 67 TYR 0.019 0.001 TYR L 50 PHE 0.022 0.002 PHE A 152 TRP 0.008 0.001 TRP H 34 HIS 0.003 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 7020) covalent geometry : angle 0.68677 ( 9591) SS BOND : bond 0.00684 ( 4) SS BOND : angle 1.48602 ( 8) hydrogen bonds : bond 0.04146 ( 244) hydrogen bonds : angle 4.60945 ( 702) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 133 time to evaluate : 0.297 Fit side-chains REVERT: H 44 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8178 (mptt) REVERT: L 24 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7773 (ttm-80) outliers start: 47 outliers final: 42 residues processed: 163 average time/residue: 0.0755 time to fit residues: 17.2298 Evaluate side-chains 174 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain L residue 1 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 45 optimal weight: 0.0570 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.172022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.143448 restraints weight = 30436.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.145471 restraints weight = 23203.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.142565 restraints weight = 10927.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143772 restraints weight = 9461.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.144072 restraints weight = 7208.752| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7024 Z= 0.121 Angle : 0.662 13.163 9599 Z= 0.324 Chirality : 0.044 0.186 1130 Planarity : 0.004 0.053 1230 Dihedral : 4.004 20.853 1002 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.41 % Favored : 92.48 % Rotamer: Outliers : 5.29 % Allowed : 33.48 % Favored : 61.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -1.43 (0.27), residues: 934 helix: 1.15 (0.32), residues: 255 sheet: -0.71 (0.38), residues: 218 loop : -2.39 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 67 TYR 0.016 0.001 TYR L 50 PHE 0.024 0.001 PHE A 152 TRP 0.006 0.001 TRP A 247 HIS 0.001 0.000 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7020) covalent geometry : angle 0.66118 ( 9591) SS BOND : bond 0.00479 ( 4) SS BOND : angle 1.31522 ( 8) hydrogen bonds : bond 0.03488 ( 244) hydrogen bonds : angle 4.43823 ( 702) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.308 Fit side-chains REVERT: A 132 SER cc_start: 0.8983 (OUTLIER) cc_final: 0.8732 (t) REVERT: H 44 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8076 (mptt) REVERT: L 24 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7781 (ttm-80) outliers start: 36 outliers final: 32 residues processed: 154 average time/residue: 0.0748 time to fit residues: 16.0313 Evaluate side-chains 166 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain L residue 1 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 89 optimal weight: 0.2980 chunk 66 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 0.0470 chunk 84 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.174902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.145395 restraints weight = 30267.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.146587 restraints weight = 21097.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.144088 restraints weight = 10025.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.145366 restraints weight = 8817.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.145583 restraints weight = 7007.192| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7024 Z= 0.107 Angle : 0.650 13.076 9599 Z= 0.317 Chirality : 0.043 0.205 1130 Planarity : 0.004 0.053 1230 Dihedral : 3.803 19.701 1002 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.66 % Favored : 93.23 % Rotamer: Outliers : 4.41 % Allowed : 34.51 % Favored : 61.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -1.30 (0.27), residues: 934 helix: 1.18 (0.32), residues: 257 sheet: -0.55 (0.38), residues: 215 loop : -2.29 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 67 TYR 0.017 0.001 TYR B 239 PHE 0.024 0.001 PHE A 152 TRP 0.006 0.001 TRP A 381 HIS 0.002 0.000 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 7020) covalent geometry : angle 0.64924 ( 9591) SS BOND : bond 0.00421 ( 4) SS BOND : angle 1.20408 ( 8) hydrogen bonds : bond 0.03088 ( 244) hydrogen bonds : angle 4.30710 ( 702) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1444.41 seconds wall clock time: 25 minutes 37.08 seconds (1537.08 seconds total)