Starting phenix.real_space_refine on Thu Mar 13 01:26:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e9w_27966/03_2025/8e9w_27966.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e9w_27966/03_2025/8e9w_27966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e9w_27966/03_2025/8e9w_27966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e9w_27966/03_2025/8e9w_27966.map" model { file = "/net/cci-nas-00/data/ceres_data/8e9w_27966/03_2025/8e9w_27966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e9w_27966/03_2025/8e9w_27966.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5451 2.51 5 N 1450 2.21 5 O 1572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8529 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2187 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1669 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain breaks: 3 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2505 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 72 Chain: "D" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 405 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1741 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'WEC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.52, per 1000 atoms: 0.65 Number of scatterers: 8529 At special positions: 0 Unit cell: (116.16, 104.72, 124.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1572 8.00 N 1450 7.00 C 5451 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 141 " - pdb=" SG CYS A 221 " distance=2.03 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 520 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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: 2.16 Conformation dependent library (CDL) restraints added in 986.9 milliseconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 37.4% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 64 through 96 removed outlier: 5.436A pdb=" N PHE A 70 " --> pdb=" O TRP A 66 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 100 Processing helix chain 'A' and resid 104 through 120 Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.656A pdb=" N ILE A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 172 removed outlier: 4.046A pdb=" N TRP A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN A 153 " --> pdb=" O CYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 181 through 198 removed outlier: 3.524A pdb=" N MET A 188 " --> pdb=" O ARG A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 230 through 240 Processing helix chain 'A' and resid 240 through 265 Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.858A pdb=" N GLN A 491 " --> pdb=" O LYS A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 517 Proline residue: A 506 - end of helix removed outlier: 3.956A pdb=" N LEU A 512 " --> pdb=" O ASN A 508 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 544 removed outlier: 3.978A pdb=" N TYR A 534 " --> pdb=" O TYR A 530 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N SER A 537 " --> pdb=" O CYS A 533 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A 538 " --> pdb=" O TYR A 534 " (cutoff:3.500A) Proline residue: A 541 - end of helix Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.532A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 45 removed outlier: 4.329A pdb=" N GLY B 45 " --> pdb=" O ASP B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 removed outlier: 4.106A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 131 through 135 removed outlier: 4.235A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 removed outlier: 3.645A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 184 through 204 removed outlier: 3.596A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 243 Processing helix chain 'C' and resid 3 through 24 removed outlier: 3.515A pdb=" N LEU C 7 " --> pdb=" O GLU C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 128 through 132 removed outlier: 4.107A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN C 132 " --> pdb=" O ARG C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 128 through 132' Processing helix chain 'D' and resid 6 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 75 removed outlier: 6.427A pdb=" N LEU B 34 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N PHE B 84 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU B 36 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N VAL B 86 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LEU B 38 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.791A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.615A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.853A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 4.387A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.623A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.697A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.746A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.045A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.516A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1621 1.33 - 1.45: 2253 1.45 - 1.57: 4760 1.57 - 1.69: 1 1.69 - 1.81: 78 Bond restraints: 8713 Sorted by residual: bond pdb=" C01 WEC A 601 " pdb=" N02 WEC A 601 " ideal model delta sigma weight residual 1.455 1.286 0.169 2.00e-02 2.50e+03 7.13e+01 bond pdb=" C06 WEC A 601 " pdb=" N07 WEC A 601 " ideal model delta sigma weight residual 1.292 1.452 -0.160 2.00e-02 2.50e+03 6.37e+01 bond pdb=" C06 WEC A 601 " pdb=" N05 WEC A 601 " ideal model delta sigma weight residual 1.373 1.499 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C03 WEC A 601 " pdb=" N02 WEC A 601 " ideal model delta sigma weight residual 1.461 1.371 0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C22 WEC A 601 " pdb=" N02 WEC A 601 " ideal model delta sigma weight residual 1.459 1.372 0.087 2.00e-02 2.50e+03 1.91e+01 ... (remaining 8708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 11632 1.92 - 3.84: 185 3.84 - 5.77: 35 5.77 - 7.69: 8 7.69 - 9.61: 5 Bond angle restraints: 11865 Sorted by residual: angle pdb=" N PHE B 167 " pdb=" CA PHE B 167 " pdb=" C PHE B 167 " ideal model delta sigma weight residual 113.18 103.57 9.61 1.21e+00 6.83e-01 6.31e+01 angle pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" N PRO E 224 " ideal model delta sigma weight residual 118.03 125.61 -7.58 1.19e+00 7.06e-01 4.06e+01 angle pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" O TYR E 223 " ideal model delta sigma weight residual 120.23 113.82 6.41 1.02e+00 9.61e-01 3.95e+01 angle pdb=" N PRO B 184 " pdb=" CA PRO B 184 " pdb=" C PRO B 184 " ideal model delta sigma weight residual 113.53 105.08 8.45 1.39e+00 5.18e-01 3.70e+01 angle pdb=" O PHE B 164 " pdb=" C PHE B 164 " pdb=" N PRO B 165 " ideal model delta sigma weight residual 120.83 114.42 6.41 1.06e+00 8.90e-01 3.66e+01 ... (remaining 11860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 4671 17.34 - 34.67: 358 34.67 - 52.01: 60 52.01 - 69.34: 11 69.34 - 86.68: 4 Dihedral angle restraints: 5104 sinusoidal: 1844 harmonic: 3260 Sorted by residual: dihedral pdb=" CB CYS A 517 " pdb=" SG CYS A 517 " pdb=" SG CYS A 520 " pdb=" CB CYS A 520 " ideal model delta sinusoidal sigma weight residual -86.00 -168.18 82.18 1 1.00e+01 1.00e-02 8.29e+01 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 147.71 -54.71 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS A 141 " pdb=" SG CYS A 141 " pdb=" SG CYS A 221 " pdb=" CB CYS A 221 " ideal model delta sinusoidal sigma weight residual -86.00 -137.28 51.28 1 1.00e+01 1.00e-02 3.60e+01 ... (remaining 5101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1176 0.059 - 0.118: 190 0.118 - 0.177: 9 0.177 - 0.236: 2 0.236 - 0.295: 1 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CA THR B 171 " pdb=" N THR B 171 " pdb=" C THR B 171 " pdb=" CB THR B 171 " both_signs ideal model delta sigma weight residual False 2.53 2.82 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA TYR E 223 " pdb=" N TYR E 223 " pdb=" C TYR E 223 " pdb=" CB TYR E 223 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ARG B 169 " pdb=" N ARG B 169 " pdb=" C ARG B 169 " pdb=" CB ARG B 169 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.44e-01 ... (remaining 1375 not shown) Planarity restraints: 1497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 171 " 0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C THR B 171 " -0.062 2.00e-02 2.50e+03 pdb=" O THR B 171 " 0.023 2.00e-02 2.50e+03 pdb=" N THR B 172 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 183 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.81e+00 pdb=" C LYS A 183 " -0.054 2.00e-02 2.50e+03 pdb=" O LYS A 183 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG A 184 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 54 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO D 55 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 55 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 55 " -0.023 5.00e-02 4.00e+02 ... (remaining 1494 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 879 2.75 - 3.29: 8307 3.29 - 3.82: 14124 3.82 - 4.36: 16892 4.36 - 4.90: 29622 Nonbonded interactions: 69824 Sorted by model distance: nonbonded pdb=" O LEU A 512 " pdb=" OG1 THR A 515 " model vdw 2.210 3.040 nonbonded pdb=" OG1 THR A 82 " pdb=" OG1 THR A 538 " model vdw 2.214 3.040 nonbonded pdb=" O LEU A 88 " pdb=" OG SER A 92 " model vdw 2.230 3.040 nonbonded pdb=" OG SER E 149 " pdb=" O LYS E 151 " model vdw 2.234 3.040 nonbonded pdb=" NH1 ARG C 49 " pdb=" O TYR C 85 " model vdw 2.243 3.120 ... (remaining 69819 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.360 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:15.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 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 : 0.005 0.169 8713 Z= 0.341 Angle : 0.628 9.611 11865 Z= 0.374 Chirality : 0.043 0.295 1378 Planarity : 0.003 0.041 1497 Dihedral : 12.691 86.677 2989 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.11 % Allowed : 0.23 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 1103 helix: 0.42 (0.27), residues: 377 sheet: 0.92 (0.32), residues: 285 loop : -0.49 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 82 HIS 0.002 0.001 HIS B 82 PHE 0.012 0.001 PHE C 234 TYR 0.016 0.001 TYR E 178 ARG 0.006 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: B 20 ASP cc_start: 0.7368 (m-30) cc_final: 0.7094 (m-30) REVERT: B 99 CYS cc_start: 0.7800 (m) cc_final: 0.7497 (m) REVERT: C 98 SER cc_start: 0.8314 (p) cc_final: 0.8111 (t) outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.9596 time to fit residues: 174.8031 Evaluate side-chains 156 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN C 125 ASN C 266 HIS E 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.131926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.113553 restraints weight = 11824.251| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.78 r_work: 0.3375 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8713 Z= 0.276 Angle : 0.581 7.951 11865 Z= 0.307 Chirality : 0.044 0.140 1378 Planarity : 0.004 0.041 1497 Dihedral : 4.690 35.635 1224 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.25 % Allowed : 9.35 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1103 helix: 1.08 (0.27), residues: 401 sheet: 0.67 (0.31), residues: 298 loop : -0.26 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 169 HIS 0.003 0.001 HIS B 209 PHE 0.012 0.002 PHE B 74 TYR 0.023 0.001 TYR E 178 ARG 0.004 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 1.407 Fit side-chains REVERT: A 88 LEU cc_start: 0.7780 (mp) cc_final: 0.7519 (mp) REVERT: B 20 ASP cc_start: 0.7909 (m-30) cc_final: 0.7537 (m-30) REVERT: B 128 ILE cc_start: 0.8404 (tp) cc_final: 0.8098 (tp) REVERT: C 98 SER cc_start: 0.8553 (p) cc_final: 0.8252 (t) REVERT: C 160 SER cc_start: 0.8270 (t) cc_final: 0.7907 (p) REVERT: E 86 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8081 (pp) REVERT: E 190 ARG cc_start: 0.8290 (ptt-90) cc_final: 0.7922 (ptt180) outliers start: 11 outliers final: 4 residues processed: 178 average time/residue: 1.3528 time to fit residues: 258.9281 Evaluate side-chains 169 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 164 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 86 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 ASN C 125 ASN E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.132662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.114109 restraints weight = 11841.404| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.80 r_work: 0.3386 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8713 Z= 0.262 Angle : 0.558 10.229 11865 Z= 0.292 Chirality : 0.044 0.136 1378 Planarity : 0.004 0.041 1497 Dihedral : 4.689 36.518 1224 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.60 % Allowed : 13.00 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.26), residues: 1103 helix: 1.15 (0.27), residues: 403 sheet: 0.48 (0.31), residues: 295 loop : -0.22 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS B 209 PHE 0.014 0.001 PHE B 74 TYR 0.021 0.001 TYR E 178 ARG 0.006 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.939 Fit side-chains REVERT: A 88 LEU cc_start: 0.7852 (mp) cc_final: 0.7615 (mp) REVERT: B 20 ASP cc_start: 0.7867 (m-30) cc_final: 0.7515 (m-30) REVERT: B 24 ARG cc_start: 0.7560 (ptp90) cc_final: 0.7357 (ptp90) REVERT: B 99 CYS cc_start: 0.8471 (m) cc_final: 0.8227 (m) REVERT: B 166 GLU cc_start: 0.7983 (mp0) cc_final: 0.7732 (mp0) REVERT: C 98 SER cc_start: 0.8576 (p) cc_final: 0.8173 (t) REVERT: E 190 ARG cc_start: 0.8306 (ptt-90) cc_final: 0.7882 (ptt180) outliers start: 14 outliers final: 8 residues processed: 173 average time/residue: 1.1976 time to fit residues: 221.5492 Evaluate side-chains 166 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 143 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 ASN C 239 ASN C 340 ASN E 167 GLN E 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.131486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.112925 restraints weight = 11744.226| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.79 r_work: 0.3358 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8713 Z= 0.353 Angle : 0.600 14.215 11865 Z= 0.311 Chirality : 0.045 0.137 1378 Planarity : 0.004 0.041 1497 Dihedral : 4.901 39.142 1224 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.51 % Allowed : 15.39 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1103 helix: 1.03 (0.27), residues: 403 sheet: 0.34 (0.30), residues: 309 loop : -0.29 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 169 HIS 0.005 0.001 HIS B 209 PHE 0.016 0.002 PHE B 74 TYR 0.021 0.002 TYR E 178 ARG 0.009 0.001 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.940 Fit side-chains REVERT: B 20 ASP cc_start: 0.7865 (m-30) cc_final: 0.7505 (m-30) REVERT: B 99 CYS cc_start: 0.8464 (m) cc_final: 0.8222 (m) REVERT: B 166 GLU cc_start: 0.8004 (mp0) cc_final: 0.7696 (mp0) REVERT: C 98 SER cc_start: 0.8592 (p) cc_final: 0.8172 (t) REVERT: E 190 ARG cc_start: 0.8282 (ptt-90) cc_final: 0.7858 (ptt180) outliers start: 22 outliers final: 13 residues processed: 184 average time/residue: 1.0616 time to fit residues: 209.5203 Evaluate side-chains 179 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 143 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 110 ASN C 239 ASN C 295 ASN E 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.131888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.113319 restraints weight = 11774.155| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.79 r_work: 0.3372 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8713 Z= 0.279 Angle : 0.574 13.700 11865 Z= 0.297 Chirality : 0.044 0.144 1378 Planarity : 0.004 0.042 1497 Dihedral : 4.806 36.882 1224 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.19 % Allowed : 16.31 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1103 helix: 1.15 (0.27), residues: 403 sheet: 0.36 (0.30), residues: 303 loop : -0.29 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS B 209 PHE 0.016 0.002 PHE E 80 TYR 0.022 0.001 TYR E 178 ARG 0.006 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: B 20 ASP cc_start: 0.7848 (m-30) cc_final: 0.7530 (m-30) REVERT: B 99 CYS cc_start: 0.8441 (m) cc_final: 0.8200 (m) REVERT: C 98 SER cc_start: 0.8577 (p) cc_final: 0.8151 (t) REVERT: E 190 ARG cc_start: 0.8281 (ptt-90) cc_final: 0.7830 (ptt180) outliers start: 28 outliers final: 18 residues processed: 181 average time/residue: 1.2351 time to fit residues: 238.4770 Evaluate side-chains 186 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 85 optimal weight: 0.7980 chunk 7 optimal weight: 0.0970 chunk 82 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 59 optimal weight: 0.0030 chunk 99 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN B 244 ASN C 110 ASN C 239 ASN E 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.133310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.114762 restraints weight = 11655.784| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.78 r_work: 0.3395 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8713 Z= 0.194 Angle : 0.530 11.296 11865 Z= 0.275 Chirality : 0.042 0.150 1378 Planarity : 0.004 0.042 1497 Dihedral : 4.581 33.531 1224 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.74 % Allowed : 17.56 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1103 helix: 1.41 (0.28), residues: 402 sheet: 0.39 (0.31), residues: 291 loop : -0.21 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE E 80 TYR 0.021 0.001 TYR E 178 ARG 0.005 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: B 20 ASP cc_start: 0.7833 (m-30) cc_final: 0.7518 (m-30) REVERT: B 99 CYS cc_start: 0.8413 (m) cc_final: 0.8167 (m) REVERT: B 147 ASP cc_start: 0.8143 (p0) cc_final: 0.7314 (p0) REVERT: B 151 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.6016 (mp0) REVERT: B 166 GLU cc_start: 0.7995 (mp0) cc_final: 0.7611 (mp0) REVERT: C 98 SER cc_start: 0.8571 (p) cc_final: 0.8137 (t) REVERT: C 293 ASN cc_start: 0.8220 (p0) cc_final: 0.8020 (p0) REVERT: E 190 ARG cc_start: 0.8264 (ptt-90) cc_final: 0.8043 (ptt180) REVERT: E 211 ASP cc_start: 0.7857 (t0) cc_final: 0.7353 (m-30) outliers start: 24 outliers final: 15 residues processed: 180 average time/residue: 1.1623 time to fit residues: 224.5995 Evaluate side-chains 186 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 101 optimal weight: 3.9990 chunk 35 optimal weight: 0.0970 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 105 optimal weight: 0.0980 chunk 47 optimal weight: 0.9990 chunk 93 optimal weight: 0.0270 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN B 244 ASN E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.134435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115992 restraints weight = 11835.965| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.81 r_work: 0.3418 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8713 Z= 0.154 Angle : 0.508 7.788 11865 Z= 0.264 Chirality : 0.042 0.142 1378 Planarity : 0.003 0.041 1497 Dihedral : 4.369 31.872 1224 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.42 % Allowed : 16.88 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1103 helix: 1.62 (0.28), residues: 398 sheet: 0.36 (0.30), residues: 297 loop : -0.13 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.002 0.001 HIS E 35 PHE 0.011 0.001 PHE B 74 TYR 0.024 0.001 TYR E 178 ARG 0.007 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 225 PHE cc_start: 0.8075 (p90) cc_final: 0.7875 (p90) REVERT: B 20 ASP cc_start: 0.7830 (m-30) cc_final: 0.7559 (m-30) REVERT: B 99 CYS cc_start: 0.8397 (m) cc_final: 0.8139 (m) REVERT: B 147 ASP cc_start: 0.8166 (p0) cc_final: 0.7318 (p0) REVERT: B 151 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.5909 (mp0) REVERT: B 200 ILE cc_start: 0.7657 (mt) cc_final: 0.7421 (mp) REVERT: C 98 SER cc_start: 0.8574 (p) cc_final: 0.8139 (t) REVERT: C 258 ASP cc_start: 0.7674 (t0) cc_final: 0.7341 (t0) REVERT: E 190 ARG cc_start: 0.8241 (ptt-90) cc_final: 0.8029 (ptt180) REVERT: E 211 ASP cc_start: 0.7914 (t0) cc_final: 0.7338 (m-30) outliers start: 30 outliers final: 15 residues processed: 176 average time/residue: 1.0167 time to fit residues: 192.8114 Evaluate side-chains 176 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 74 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 81 optimal weight: 0.0470 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.133211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.114596 restraints weight = 11954.052| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.82 r_work: 0.3396 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8713 Z= 0.209 Angle : 0.531 8.462 11865 Z= 0.276 Chirality : 0.043 0.166 1378 Planarity : 0.004 0.041 1497 Dihedral : 4.478 33.223 1224 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.96 % Allowed : 18.02 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1103 helix: 1.55 (0.28), residues: 402 sheet: 0.44 (0.31), residues: 297 loop : -0.15 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE B 74 TYR 0.021 0.001 TYR E 178 ARG 0.010 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 131 MET cc_start: 0.7534 (ttm) cc_final: 0.7328 (ptm) REVERT: A 225 PHE cc_start: 0.8039 (p90) cc_final: 0.7797 (p90) REVERT: B 20 ASP cc_start: 0.7862 (m-30) cc_final: 0.7576 (m-30) REVERT: B 99 CYS cc_start: 0.8408 (m) cc_final: 0.8165 (m) REVERT: B 147 ASP cc_start: 0.8124 (p0) cc_final: 0.7300 (p0) REVERT: B 151 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.5983 (mp0) REVERT: C 98 SER cc_start: 0.8574 (p) cc_final: 0.8135 (t) REVERT: C 258 ASP cc_start: 0.7714 (t0) cc_final: 0.7463 (t0) REVERT: E 190 ARG cc_start: 0.8265 (ptt-90) cc_final: 0.8046 (ptt180) REVERT: E 211 ASP cc_start: 0.7923 (t0) cc_final: 0.7369 (m-30) outliers start: 26 outliers final: 17 residues processed: 179 average time/residue: 1.1533 time to fit residues: 221.9610 Evaluate side-chains 184 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 6 optimal weight: 0.0270 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 125 ASN C 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.133482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114909 restraints weight = 11833.872| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.81 r_work: 0.3402 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8713 Z= 0.208 Angle : 0.537 8.621 11865 Z= 0.280 Chirality : 0.043 0.165 1378 Planarity : 0.004 0.047 1497 Dihedral : 4.484 33.173 1224 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.85 % Allowed : 17.79 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 1103 helix: 1.54 (0.28), residues: 402 sheet: 0.45 (0.31), residues: 296 loop : -0.16 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE A 225 TYR 0.020 0.001 TYR E 178 ARG 0.012 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 225 PHE cc_start: 0.8038 (p90) cc_final: 0.7819 (p90) REVERT: B 20 ASP cc_start: 0.7864 (m-30) cc_final: 0.7582 (m-30) REVERT: B 99 CYS cc_start: 0.8398 (m) cc_final: 0.8154 (m) REVERT: B 147 ASP cc_start: 0.8119 (p0) cc_final: 0.7327 (p0) REVERT: B 151 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6035 (mp0) REVERT: C 98 SER cc_start: 0.8570 (p) cc_final: 0.8149 (t) REVERT: E 137 VAL cc_start: 0.8294 (t) cc_final: 0.7991 (p) REVERT: E 190 ARG cc_start: 0.8256 (ptt-90) cc_final: 0.8036 (ptt180) REVERT: E 211 ASP cc_start: 0.7915 (t0) cc_final: 0.7349 (m-30) outliers start: 25 outliers final: 17 residues processed: 179 average time/residue: 1.1557 time to fit residues: 222.3378 Evaluate side-chains 183 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 110 ASN C 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.132350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113774 restraints weight = 11749.525| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.79 r_work: 0.3387 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8713 Z= 0.264 Angle : 0.566 10.667 11865 Z= 0.294 Chirality : 0.044 0.187 1378 Planarity : 0.004 0.048 1497 Dihedral : 4.630 34.458 1224 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.39 % Allowed : 19.27 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1103 helix: 1.44 (0.28), residues: 402 sheet: 0.34 (0.30), residues: 302 loop : -0.12 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE E 80 TYR 0.019 0.001 TYR E 178 ARG 0.012 0.000 ARG B 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 225 PHE cc_start: 0.8061 (p90) cc_final: 0.7792 (p90) REVERT: B 20 ASP cc_start: 0.7860 (m-30) cc_final: 0.7590 (m-30) REVERT: B 99 CYS cc_start: 0.8405 (m) cc_final: 0.8161 (m) REVERT: B 147 ASP cc_start: 0.8119 (p0) cc_final: 0.7392 (p0) REVERT: B 151 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6101 (mp0) REVERT: C 98 SER cc_start: 0.8578 (p) cc_final: 0.8152 (t) REVERT: C 258 ASP cc_start: 0.7666 (t0) cc_final: 0.7401 (t0) REVERT: E 190 ARG cc_start: 0.8271 (ptt-90) cc_final: 0.8037 (ptt180) REVERT: E 211 ASP cc_start: 0.7899 (t0) cc_final: 0.7369 (m-30) outliers start: 21 outliers final: 14 residues processed: 165 average time/residue: 1.0721 time to fit residues: 189.4355 Evaluate side-chains 171 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 91 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.133175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114609 restraints weight = 11816.217| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.80 r_work: 0.3396 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8713 Z= 0.208 Angle : 0.542 9.670 11865 Z= 0.282 Chirality : 0.043 0.163 1378 Planarity : 0.004 0.044 1497 Dihedral : 4.518 33.174 1224 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.28 % Allowed : 19.27 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1103 helix: 1.54 (0.28), residues: 401 sheet: 0.36 (0.31), residues: 291 loop : -0.12 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE E 80 TYR 0.020 0.001 TYR E 178 ARG 0.011 0.000 ARG B 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7622.19 seconds wall clock time: 133 minutes 56.47 seconds (8036.47 seconds total)