Starting phenix.real_space_refine on Sun May 11 20:28:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fn0_29302/05_2025/8fn0_29302.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fn0_29302/05_2025/8fn0_29302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fn0_29302/05_2025/8fn0_29302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fn0_29302/05_2025/8fn0_29302.map" model { file = "/net/cci-nas-00/data/ceres_data/8fn0_29302/05_2025/8fn0_29302.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fn0_29302/05_2025/8fn0_29302.cif" } resolution = 2.89 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= 0.002 sd= 0.025 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: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 5431 2.51 5 N 1424 2.21 5 O 1589 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8502 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2074 Classifications: {'peptide': 282} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 272} Chain breaks: 2 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "C" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2568 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 378 Classifications: {'peptide': 51} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1635 Classifications: {'peptide': 212} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 207} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1756 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'SRW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.30, per 1000 atoms: 0.62 Number of scatterers: 8502 At special positions: 0 Unit cell: (91.52, 117.92, 132.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 F 1 9.00 O 1589 8.00 N 1424 7.00 C 5431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 225 " 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: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 37.7% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 60 through 90 Processing helix chain 'A' and resid 101 through 129 Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 137 through 173 removed outlier: 3.503A pdb=" N GLY A 141 " --> pdb=" O PHE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 removed outlier: 3.768A pdb=" N THR A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 202 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 230 through 246 Processing helix chain 'A' and resid 246 through 266 Processing helix chain 'A' and resid 302 through 334 Proline residue: A 323 - end of helix Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 340 through 373 removed outlier: 3.859A pdb=" N SER A 362 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Proline residue: A 366 - end of helix Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 29 through 37 removed outlier: 4.496A pdb=" N THR C 34 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ASN C 35 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN C 36 " --> pdb=" O ILE C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.992A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.319A 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 12 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'B' and resid 3 through 28 Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 91 through 95 removed outlier: 4.366A pdb=" N HIS B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 91 through 95' Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 116 through 127 Processing helix chain 'B' and resid 142 through 150 removed outlier: 4.761A pdb=" N GLU B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 181 Processing helix chain 'B' and resid 202 through 220 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.738A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 212 Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.812A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.645A 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: 3.574A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.559A 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: 6.993A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.767A 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: 3.622A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.601A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.443A 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: 3.600A pdb=" N ALA C 231 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.677A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 51 through 52 removed outlier: 6.263A pdb=" N VAL B 31 " --> pdb=" O ARG B 79 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N PHE B 81 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU B 33 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 9.437A pdb=" N ALA B 102 " --> pdb=" O ASP B 30 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS B 32 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE B 104 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU B 34 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS B 106 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU B 36 " --> pdb=" O CYS B 106 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N ASP B 108 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE B 103 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N PHE B 139 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE B 105 " --> pdb=" O PHE B 139 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASN B 141 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 107 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.974A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.360A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 136 removed outlier: 4.121A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1254 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: 2.46 Time building geometry restraints manager: 2.81 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: 2374 1.33 - 1.45: 1630 1.45 - 1.57: 4594 1.57 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 8680 Sorted by residual: bond pdb=" N LEU A 371 " pdb=" CA LEU A 371 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.17e-02 7.31e+03 1.11e+01 bond pdb=" N VAL A 372 " pdb=" CA VAL A 372 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.19e-02 7.06e+03 1.08e+01 bond pdb=" C VAL E 135 " pdb=" N PRO E 136 " ideal model delta sigma weight residual 1.332 1.373 -0.041 1.33e-02 5.65e+03 9.54e+00 bond pdb=" N ILE A 364 " pdb=" CA ILE A 364 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.34e-02 5.57e+03 9.50e+00 bond pdb=" N VAL E 137 " pdb=" CA VAL E 137 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.14e-02 7.69e+03 9.29e+00 ... (remaining 8675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 11209 2.05 - 4.11: 536 4.11 - 6.16: 38 6.16 - 8.21: 10 8.21 - 10.27: 7 Bond angle restraints: 11800 Sorted by residual: angle pdb=" CA MET B 115 " pdb=" C MET B 115 " pdb=" O MET B 115 " ideal model delta sigma weight residual 121.99 113.37 8.62 1.14e+00 7.69e-01 5.72e+01 angle pdb=" N PRO E 136 " pdb=" CA PRO E 136 " pdb=" C PRO E 136 " ideal model delta sigma weight residual 111.11 100.84 10.27 1.59e+00 3.96e-01 4.17e+01 angle pdb=" N CYS B 222 " pdb=" CA CYS B 222 " pdb=" C CYS B 222 " ideal model delta sigma weight residual 113.16 105.24 7.92 1.24e+00 6.50e-01 4.08e+01 angle pdb=" CA ILE A 364 " pdb=" CB ILE A 364 " pdb=" CG1 ILE A 364 " ideal model delta sigma weight residual 110.40 119.83 -9.43 1.70e+00 3.46e-01 3.07e+01 angle pdb=" CA ILE A 367 " pdb=" CB ILE A 367 " pdb=" CG1 ILE A 367 " ideal model delta sigma weight residual 110.40 119.82 -9.42 1.70e+00 3.46e-01 3.07e+01 ... (remaining 11795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.17: 5035 29.17 - 58.35: 52 58.35 - 87.52: 22 87.52 - 116.70: 2 116.70 - 145.87: 3 Dihedral angle restraints: 5114 sinusoidal: 1878 harmonic: 3236 Sorted by residual: dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 225 " pdb=" CB CYS A 225 " ideal model delta sinusoidal sigma weight residual 93.00 159.95 -66.95 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" C25 SRW A 501 " pdb=" C24 SRW A 501 " pdb=" C26 SRW A 501 " pdb=" F1 SRW A 501 " ideal model delta sinusoidal sigma weight residual 106.02 -108.11 -145.87 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C14 SRW A 501 " pdb=" C24 SRW A 501 " pdb=" C26 SRW A 501 " pdb=" C25 SRW A 501 " ideal model delta sinusoidal sigma weight residual 110.71 -109.31 -139.98 1 3.00e+01 1.11e-03 1.88e+01 ... (remaining 5111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.990: 1368 0.990 - 1.979: 2 1.979 - 2.969: 0 2.969 - 3.959: 0 3.959 - 4.948: 1 Chirality restraints: 1371 Sorted by residual: chirality pdb=" C8 SRW A 501 " pdb=" C12 SRW A 501 " pdb=" C3 SRW A 501 " pdb=" C9 SRW A 501 " both_signs ideal model delta sigma weight residual False -2.46 2.49 -4.95 2.00e-01 2.50e+01 6.12e+02 chirality pdb=" CB ILE A 367 " pdb=" CA ILE A 367 " pdb=" CG1 ILE A 367 " pdb=" CG2 ILE A 367 " both_signs ideal model delta sigma weight residual False 2.64 0.82 1.83 2.00e-01 2.50e+01 8.34e+01 chirality pdb=" CB ILE A 364 " pdb=" CA ILE A 364 " pdb=" CG1 ILE A 364 " pdb=" CG2 ILE A 364 " both_signs ideal model delta sigma weight residual False 2.64 0.82 1.82 2.00e-01 2.50e+01 8.30e+01 ... (remaining 1368 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 122 " -0.026 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C PRO A 122 " 0.089 2.00e-02 2.50e+03 pdb=" O PRO A 122 " -0.033 2.00e-02 2.50e+03 pdb=" N VAL A 123 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 124 " 0.022 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C GLU A 124 " -0.074 2.00e-02 2.50e+03 pdb=" O GLU A 124 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU A 125 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 136 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.66e+01 pdb=" C PRO E 136 " 0.070 2.00e-02 2.50e+03 pdb=" O PRO E 136 " -0.027 2.00e-02 2.50e+03 pdb=" N VAL E 137 " -0.024 2.00e-02 2.50e+03 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1449 2.76 - 3.29: 8161 3.29 - 3.83: 14101 3.83 - 4.36: 16917 4.36 - 4.90: 29644 Nonbonded interactions: 70272 Sorted by model distance: nonbonded pdb=" O MET C 325 " pdb=" ND2 ASN C 340 " model vdw 2.225 3.120 nonbonded pdb=" OH TYR A 154 " pdb=" OD1 ASN A 241 " model vdw 2.322 3.040 nonbonded pdb=" OE1 GLU C 130 " pdb=" NH2 ARG C 134 " model vdw 2.322 3.120 nonbonded pdb=" ND1 HIS D 44 " pdb=" OE2 GLU D 47 " model vdw 2.328 3.120 nonbonded pdb=" NE ARG E 148 " pdb=" O THR E 198 " model vdw 2.339 3.120 ... (remaining 70267 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: 0.010 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.010 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.670 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:9.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 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 0.060 8682 Z= 0.290 Angle : 0.949 10.266 11804 Z= 0.612 Chirality : 0.159 4.948 1371 Planarity : 0.006 0.084 1486 Dihedral : 11.788 145.870 3022 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.11 % Allowed : 1.36 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.24), residues: 1098 helix: 0.92 (0.25), residues: 373 sheet: 1.03 (0.28), residues: 307 loop : 0.65 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP E 111 HIS 0.008 0.002 HIS C 91 PHE 0.023 0.003 PHE A 317 TYR 0.025 0.003 TYR E 102 ARG 0.015 0.001 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.14148 ( 446) hydrogen bonds : angle 6.50132 ( 1254) SS BOND : bond 0.00256 ( 2) SS BOND : angle 2.49987 ( 4) covalent geometry : bond 0.00514 ( 8680) covalent geometry : angle 0.94799 (11800) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.7888 (mt) cc_final: 0.7675 (tm) REVERT: A 238 ILE cc_start: 0.7891 (tp) cc_final: 0.7662 (tp) REVERT: A 250 MET cc_start: 0.7103 (tpp) cc_final: 0.6826 (tpt) REVERT: A 343 LEU cc_start: 0.8181 (tp) cc_final: 0.7864 (tt) REVERT: A 350 PHE cc_start: 0.7245 (t80) cc_final: 0.6821 (t80) REVERT: C 37 ILE cc_start: 0.8089 (mt) cc_final: 0.7822 (pt) REVERT: C 38 ASP cc_start: 0.7789 (m-30) cc_final: 0.7575 (m-30) REVERT: C 227 SER cc_start: 0.8406 (t) cc_final: 0.8106 (m) REVERT: C 262 MET cc_start: 0.8018 (tpp) cc_final: 0.7713 (tpp) REVERT: C 314 ARG cc_start: 0.8538 (ttm170) cc_final: 0.8186 (ttm170) REVERT: B 32 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8572 (mtmp) REVERT: B 66 ILE cc_start: 0.8160 (mt) cc_final: 0.7937 (mm) REVERT: E 17 SER cc_start: 0.8268 (p) cc_final: 0.7995 (m) REVERT: E 23 SER cc_start: 0.8303 (t) cc_final: 0.8043 (m) REVERT: E 25 SER cc_start: 0.8304 (t) cc_final: 0.8079 (p) REVERT: E 192 SER cc_start: 0.8549 (t) cc_final: 0.8330 (p) REVERT: E 211 ASP cc_start: 0.7989 (t0) cc_final: 0.7692 (t0) REVERT: E 218 MET cc_start: 0.8279 (ttp) cc_final: 0.7915 (ttp) outliers start: 1 outliers final: 1 residues processed: 223 average time/residue: 0.7270 time to fit residues: 179.1808 Evaluate side-chains 187 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 HIS C 91 HIS C 132 ASN C 268 ASN B 70 HIS B 95 HIS B 128 ASN B 141 ASN B 201 ASN B 202 ASN E 77 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.135675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.114175 restraints weight = 12536.130| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.14 r_work: 0.3400 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8682 Z= 0.170 Angle : 0.601 8.585 11804 Z= 0.325 Chirality : 0.044 0.185 1371 Planarity : 0.004 0.036 1486 Dihedral : 11.044 147.771 1225 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.16 % Allowed : 7.95 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.25), residues: 1098 helix: 2.39 (0.26), residues: 364 sheet: 1.16 (0.29), residues: 294 loop : 0.46 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 321 HIS 0.006 0.001 HIS A 325 PHE 0.018 0.002 PHE C 199 TYR 0.025 0.002 TYR A 349 ARG 0.005 0.001 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.05218 ( 446) hydrogen bonds : angle 4.92589 ( 1254) SS BOND : bond 0.00224 ( 2) SS BOND : angle 1.23141 ( 4) covalent geometry : bond 0.00379 ( 8680) covalent geometry : angle 0.60079 (11800) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 128 PHE cc_start: 0.7004 (m-80) cc_final: 0.6715 (m-80) REVERT: A 250 MET cc_start: 0.7120 (tpp) cc_final: 0.6802 (tpt) REVERT: A 343 LEU cc_start: 0.7971 (tp) cc_final: 0.7679 (tt) REVERT: A 350 PHE cc_start: 0.7118 (t80) cc_final: 0.6696 (t80) REVERT: A 364 ILE cc_start: 0.8037 (mm) cc_final: 0.7823 (pp) REVERT: C 37 ILE cc_start: 0.7967 (mt) cc_final: 0.7544 (pt) REVERT: C 38 ASP cc_start: 0.8017 (m-30) cc_final: 0.7759 (m-30) REVERT: C 49 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7601 (mpt-90) REVERT: C 55 LEU cc_start: 0.8573 (mt) cc_final: 0.8368 (mt) REVERT: C 158 VAL cc_start: 0.8412 (p) cc_final: 0.8027 (t) REVERT: C 214 ARG cc_start: 0.7415 (mpt180) cc_final: 0.6797 (mpt180) REVERT: B 66 ILE cc_start: 0.8113 (mt) cc_final: 0.7879 (mm) REVERT: B 124 SER cc_start: 0.8514 (t) cc_final: 0.8235 (p) REVERT: E 17 SER cc_start: 0.8087 (p) cc_final: 0.7844 (m) REVERT: E 23 SER cc_start: 0.8250 (t) cc_final: 0.7968 (m) REVERT: E 63 THR cc_start: 0.8352 (p) cc_final: 0.8147 (t) REVERT: E 93 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8187 (tpp) REVERT: E 129 THR cc_start: 0.8334 (m) cc_final: 0.7800 (p) REVERT: E 192 SER cc_start: 0.8672 (t) cc_final: 0.8396 (p) REVERT: E 211 ASP cc_start: 0.7952 (t0) cc_final: 0.7628 (t0) outliers start: 19 outliers final: 12 residues processed: 210 average time/residue: 0.6753 time to fit residues: 157.0595 Evaluate side-chains 203 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 189 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 106 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN C 340 ASN B 202 ASN E 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.135798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.114118 restraints weight = 12666.226| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.17 r_work: 0.3397 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8682 Z= 0.155 Angle : 0.564 8.630 11804 Z= 0.301 Chirality : 0.043 0.260 1371 Planarity : 0.004 0.041 1486 Dihedral : 10.648 147.985 1223 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.50 % Allowed : 10.78 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.25), residues: 1098 helix: 2.60 (0.27), residues: 365 sheet: 1.23 (0.29), residues: 293 loop : 0.31 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 321 HIS 0.006 0.001 HIS A 325 PHE 0.017 0.002 PHE B 207 TYR 0.015 0.002 TYR E 178 ARG 0.007 0.001 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.04755 ( 446) hydrogen bonds : angle 4.65733 ( 1254) SS BOND : bond 0.00168 ( 2) SS BOND : angle 0.91219 ( 4) covalent geometry : bond 0.00346 ( 8680) covalent geometry : angle 0.56369 (11800) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 128 PHE cc_start: 0.7056 (m-80) cc_final: 0.6787 (m-80) REVERT: A 250 MET cc_start: 0.7102 (tpp) cc_final: 0.6861 (tpt) REVERT: C 158 VAL cc_start: 0.8455 (p) cc_final: 0.8079 (t) REVERT: C 217 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7401 (ppp) REVERT: C 219 ARG cc_start: 0.8315 (mtt-85) cc_final: 0.8075 (mtt90) REVERT: B 66 ILE cc_start: 0.8189 (mt) cc_final: 0.7954 (mm) REVERT: B 108 ASP cc_start: 0.7653 (t0) cc_final: 0.7398 (t0) REVERT: B 124 SER cc_start: 0.8512 (t) cc_final: 0.8257 (p) REVERT: E 17 SER cc_start: 0.8069 (p) cc_final: 0.7843 (m) REVERT: E 23 SER cc_start: 0.8258 (t) cc_final: 0.7964 (m) REVERT: E 93 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8080 (tpp) REVERT: E 129 THR cc_start: 0.8336 (m) cc_final: 0.7790 (p) REVERT: E 154 LEU cc_start: 0.8259 (tt) cc_final: 0.8042 (tp) REVERT: E 192 SER cc_start: 0.8600 (t) cc_final: 0.8342 (p) REVERT: E 200 PHE cc_start: 0.8503 (m-80) cc_final: 0.8189 (m-80) REVERT: E 211 ASP cc_start: 0.7918 (t0) cc_final: 0.7598 (t0) outliers start: 22 outliers final: 15 residues processed: 205 average time/residue: 0.7303 time to fit residues: 164.9828 Evaluate side-chains 204 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 14 optimal weight: 0.0030 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.136082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.114473 restraints weight = 12679.809| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.17 r_work: 0.3404 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8682 Z= 0.143 Angle : 0.546 8.177 11804 Z= 0.291 Chirality : 0.043 0.260 1371 Planarity : 0.004 0.037 1486 Dihedral : 10.475 148.038 1223 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.50 % Allowed : 12.60 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.25), residues: 1098 helix: 2.66 (0.27), residues: 365 sheet: 1.23 (0.29), residues: 291 loop : 0.18 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 135 HIS 0.005 0.001 HIS A 325 PHE 0.017 0.002 PHE A 147 TYR 0.014 0.001 TYR E 178 ARG 0.007 0.001 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.04515 ( 446) hydrogen bonds : angle 4.57774 ( 1254) SS BOND : bond 0.00091 ( 2) SS BOND : angle 0.86851 ( 4) covalent geometry : bond 0.00317 ( 8680) covalent geometry : angle 0.54576 (11800) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 1.051 Fit side-chains REVERT: A 128 PHE cc_start: 0.7088 (m-80) cc_final: 0.6843 (m-80) REVERT: A 250 MET cc_start: 0.7088 (tpp) cc_final: 0.6859 (tpt) REVERT: C 49 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7505 (mpt-90) REVERT: C 158 VAL cc_start: 0.8438 (p) cc_final: 0.8076 (t) REVERT: C 217 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7383 (ppp) REVERT: C 219 ARG cc_start: 0.8342 (mtt-85) cc_final: 0.8141 (mtt90) REVERT: B 66 ILE cc_start: 0.8198 (mt) cc_final: 0.7949 (mm) REVERT: B 108 ASP cc_start: 0.7636 (t0) cc_final: 0.7359 (t0) REVERT: B 208 ASP cc_start: 0.8075 (m-30) cc_final: 0.7828 (m-30) REVERT: E 17 SER cc_start: 0.8038 (p) cc_final: 0.7831 (m) REVERT: E 23 SER cc_start: 0.8249 (t) cc_final: 0.7943 (m) REVERT: E 93 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8088 (tpp) REVERT: E 129 THR cc_start: 0.8352 (m) cc_final: 0.7786 (p) REVERT: E 154 LEU cc_start: 0.8262 (tt) cc_final: 0.8047 (tp) REVERT: E 192 SER cc_start: 0.8597 (t) cc_final: 0.8339 (p) REVERT: E 200 PHE cc_start: 0.8474 (m-80) cc_final: 0.8106 (m-80) REVERT: E 211 ASP cc_start: 0.7934 (t0) cc_final: 0.7573 (t0) outliers start: 22 outliers final: 13 residues processed: 195 average time/residue: 0.7095 time to fit residues: 152.5828 Evaluate side-chains 205 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 91 optimal weight: 0.0980 chunk 77 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.135923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.113997 restraints weight = 12474.400| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.15 r_work: 0.3399 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8682 Z= 0.145 Angle : 0.540 8.430 11804 Z= 0.288 Chirality : 0.042 0.256 1371 Planarity : 0.004 0.038 1486 Dihedral : 10.496 148.186 1223 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.06 % Allowed : 12.26 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.26), residues: 1098 helix: 2.66 (0.27), residues: 366 sheet: 1.22 (0.30), residues: 289 loop : 0.07 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 135 HIS 0.005 0.001 HIS A 325 PHE 0.020 0.002 PHE A 147 TYR 0.014 0.001 TYR E 178 ARG 0.007 0.001 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 446) hydrogen bonds : angle 4.54588 ( 1254) SS BOND : bond 0.00131 ( 2) SS BOND : angle 0.91156 ( 4) covalent geometry : bond 0.00325 ( 8680) covalent geometry : angle 0.53940 (11800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 128 PHE cc_start: 0.7057 (m-80) cc_final: 0.6847 (m-80) REVERT: A 250 MET cc_start: 0.7034 (tpp) cc_final: 0.6784 (tpt) REVERT: A 259 VAL cc_start: 0.8281 (t) cc_final: 0.8031 (t) REVERT: C 49 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7458 (mpt-90) REVERT: C 158 VAL cc_start: 0.8450 (p) cc_final: 0.8092 (t) REVERT: C 217 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7332 (ppp) REVERT: C 219 ARG cc_start: 0.8372 (mtt-85) cc_final: 0.8159 (mtt90) REVERT: B 66 ILE cc_start: 0.8198 (mt) cc_final: 0.7948 (mm) REVERT: B 108 ASP cc_start: 0.7627 (t0) cc_final: 0.7329 (t0) REVERT: B 224 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7499 (tp) REVERT: E 23 SER cc_start: 0.8225 (t) cc_final: 0.7930 (m) REVERT: E 93 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.8088 (tpp) REVERT: E 129 THR cc_start: 0.8338 (m) cc_final: 0.7760 (p) REVERT: E 154 LEU cc_start: 0.8322 (tt) cc_final: 0.8114 (tp) REVERT: E 192 SER cc_start: 0.8592 (t) cc_final: 0.8330 (p) REVERT: E 200 PHE cc_start: 0.8463 (m-80) cc_final: 0.8187 (m-80) REVERT: E 211 ASP cc_start: 0.7907 (t0) cc_final: 0.7524 (t0) outliers start: 27 outliers final: 16 residues processed: 197 average time/residue: 0.7077 time to fit residues: 154.3037 Evaluate side-chains 201 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.135413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.113626 restraints weight = 12406.602| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.15 r_work: 0.3389 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8682 Z= 0.168 Angle : 0.570 8.625 11804 Z= 0.302 Chirality : 0.043 0.252 1371 Planarity : 0.004 0.037 1486 Dihedral : 10.847 148.398 1223 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.50 % Allowed : 13.51 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.25), residues: 1098 helix: 2.52 (0.27), residues: 367 sheet: 1.18 (0.30), residues: 289 loop : -0.06 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 135 HIS 0.006 0.001 HIS A 325 PHE 0.020 0.002 PHE B 146 TYR 0.013 0.001 TYR E 178 ARG 0.004 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 446) hydrogen bonds : angle 4.61871 ( 1254) SS BOND : bond 0.00223 ( 2) SS BOND : angle 1.09575 ( 4) covalent geometry : bond 0.00381 ( 8680) covalent geometry : angle 0.56997 (11800) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 204 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6531 (tmt) REVERT: A 250 MET cc_start: 0.7063 (tpp) cc_final: 0.6860 (tpt) REVERT: A 259 VAL cc_start: 0.8293 (t) cc_final: 0.8031 (t) REVERT: C 158 VAL cc_start: 0.8425 (p) cc_final: 0.8086 (t) REVERT: C 217 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7287 (ppp) REVERT: C 219 ARG cc_start: 0.8380 (mtt-85) cc_final: 0.8091 (mtt90) REVERT: B 108 ASP cc_start: 0.7630 (t0) cc_final: 0.7314 (t0) REVERT: B 208 ASP cc_start: 0.8064 (m-30) cc_final: 0.7812 (m-30) REVERT: E 23 SER cc_start: 0.8223 (t) cc_final: 0.7932 (m) REVERT: E 93 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8097 (tpp) REVERT: E 110 PHE cc_start: 0.8584 (t80) cc_final: 0.8149 (t80) REVERT: E 129 THR cc_start: 0.8355 (m) cc_final: 0.7781 (p) REVERT: E 154 LEU cc_start: 0.8329 (tt) cc_final: 0.8128 (tp) REVERT: E 192 SER cc_start: 0.8610 (t) cc_final: 0.8348 (p) REVERT: E 200 PHE cc_start: 0.8458 (m-80) cc_final: 0.8210 (m-80) REVERT: E 211 ASP cc_start: 0.7925 (t0) cc_final: 0.7539 (t0) outliers start: 22 outliers final: 15 residues processed: 191 average time/residue: 0.6861 time to fit residues: 145.0528 Evaluate side-chains 202 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 25 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 59 optimal weight: 0.3980 chunk 89 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 182 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.138078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.116025 restraints weight = 12401.918| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.18 r_work: 0.3407 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8682 Z= 0.124 Angle : 0.539 9.159 11804 Z= 0.286 Chirality : 0.042 0.251 1371 Planarity : 0.004 0.037 1486 Dihedral : 10.560 148.404 1223 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.16 % Allowed : 14.07 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.26), residues: 1098 helix: 2.60 (0.27), residues: 367 sheet: 1.06 (0.29), residues: 299 loop : -0.06 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 135 HIS 0.004 0.001 HIS A 325 PHE 0.020 0.002 PHE B 146 TYR 0.014 0.001 TYR E 178 ARG 0.005 0.000 ARG F 9 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 446) hydrogen bonds : angle 4.54779 ( 1254) SS BOND : bond 0.00078 ( 2) SS BOND : angle 0.78021 ( 4) covalent geometry : bond 0.00275 ( 8680) covalent geometry : angle 0.53923 (11800) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6509 (tmt) REVERT: A 259 VAL cc_start: 0.8269 (t) cc_final: 0.8024 (t) REVERT: C 49 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7456 (mpt-90) REVERT: C 158 VAL cc_start: 0.8481 (p) cc_final: 0.8057 (t) REVERT: B 108 ASP cc_start: 0.7648 (t0) cc_final: 0.7321 (t0) REVERT: E 23 SER cc_start: 0.8202 (t) cc_final: 0.7913 (m) REVERT: E 93 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8089 (tpp) REVERT: E 110 PHE cc_start: 0.8530 (t80) cc_final: 0.8100 (t80) REVERT: E 129 THR cc_start: 0.8376 (m) cc_final: 0.7789 (p) REVERT: E 192 SER cc_start: 0.8558 (t) cc_final: 0.8291 (p) REVERT: E 200 PHE cc_start: 0.8436 (m-80) cc_final: 0.8088 (m-80) REVERT: E 211 ASP cc_start: 0.7885 (t0) cc_final: 0.7496 (t0) outliers start: 19 outliers final: 12 residues processed: 195 average time/residue: 0.7491 time to fit residues: 161.5379 Evaluate side-chains 196 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 57 optimal weight: 0.0870 chunk 93 optimal weight: 2.9990 chunk 94 optimal weight: 0.0020 overall best weight: 0.4366 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.137742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.115672 restraints weight = 12521.000| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.18 r_work: 0.3418 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8682 Z= 0.118 Angle : 0.547 9.508 11804 Z= 0.286 Chirality : 0.042 0.242 1371 Planarity : 0.003 0.039 1486 Dihedral : 10.335 148.666 1223 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.04 % Allowed : 14.64 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.26), residues: 1098 helix: 2.57 (0.27), residues: 368 sheet: 1.03 (0.29), residues: 301 loop : -0.03 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 135 HIS 0.004 0.001 HIS A 325 PHE 0.019 0.002 PHE B 207 TYR 0.014 0.001 TYR E 178 ARG 0.006 0.000 ARG F 9 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 446) hydrogen bonds : angle 4.49381 ( 1254) SS BOND : bond 0.00067 ( 2) SS BOND : angle 0.70059 ( 4) covalent geometry : bond 0.00256 ( 8680) covalent geometry : angle 0.54656 (11800) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 204 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6465 (tmt) REVERT: A 241 ASN cc_start: 0.7551 (t0) cc_final: 0.7233 (t0) REVERT: A 259 VAL cc_start: 0.8267 (t) cc_final: 0.8007 (t) REVERT: C 49 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7445 (mpt-90) REVERT: C 98 SER cc_start: 0.8355 (p) cc_final: 0.7937 (t) REVERT: C 158 VAL cc_start: 0.8479 (p) cc_final: 0.8049 (t) REVERT: C 217 MET cc_start: 0.8246 (ppp) cc_final: 0.8043 (pmm) REVERT: C 264 TYR cc_start: 0.8449 (m-80) cc_final: 0.8215 (m-80) REVERT: B 108 ASP cc_start: 0.7653 (t0) cc_final: 0.7320 (t0) REVERT: E 23 SER cc_start: 0.8196 (t) cc_final: 0.7906 (m) REVERT: E 93 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8063 (tpp) REVERT: E 110 PHE cc_start: 0.8522 (t80) cc_final: 0.8093 (t80) REVERT: E 129 THR cc_start: 0.8370 (m) cc_final: 0.7798 (p) REVERT: E 192 SER cc_start: 0.8528 (t) cc_final: 0.8265 (p) REVERT: E 200 PHE cc_start: 0.8401 (m-80) cc_final: 0.8109 (m-80) REVERT: E 211 ASP cc_start: 0.7872 (t0) cc_final: 0.7483 (t0) outliers start: 18 outliers final: 12 residues processed: 192 average time/residue: 0.7333 time to fit residues: 155.2118 Evaluate side-chains 196 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 0.0000 chunk 107 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 0.3980 chunk 74 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN A 365 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.136953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114849 restraints weight = 12547.105| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.19 r_work: 0.3409 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8682 Z= 0.136 Angle : 0.551 9.449 11804 Z= 0.291 Chirality : 0.042 0.231 1371 Planarity : 0.004 0.037 1486 Dihedral : 10.383 148.917 1223 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.84 % Allowed : 14.53 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.26), residues: 1098 helix: 2.54 (0.27), residues: 368 sheet: 1.03 (0.29), residues: 301 loop : -0.04 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 135 HIS 0.005 0.001 HIS A 325 PHE 0.021 0.002 PHE B 207 TYR 0.013 0.001 TYR E 178 ARG 0.006 0.000 ARG F 9 Details of bonding type rmsd hydrogen bonds : bond 0.04125 ( 446) hydrogen bonds : angle 4.53281 ( 1254) SS BOND : bond 0.00078 ( 2) SS BOND : angle 0.82047 ( 4) covalent geometry : bond 0.00305 ( 8680) covalent geometry : angle 0.55039 (11800) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6483 (tmt) REVERT: A 241 ASN cc_start: 0.7561 (t0) cc_final: 0.7229 (t0) REVERT: A 259 VAL cc_start: 0.8286 (t) cc_final: 0.8009 (t) REVERT: C 49 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7434 (mpt-90) REVERT: C 98 SER cc_start: 0.8359 (p) cc_final: 0.7936 (t) REVERT: C 158 VAL cc_start: 0.8485 (p) cc_final: 0.8052 (t) REVERT: C 264 TYR cc_start: 0.8468 (m-80) cc_final: 0.8248 (m-80) REVERT: B 108 ASP cc_start: 0.7638 (t0) cc_final: 0.7281 (t0) REVERT: B 170 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.7176 (m-30) REVERT: E 23 SER cc_start: 0.8207 (t) cc_final: 0.7910 (m) REVERT: E 93 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8069 (tpp) REVERT: E 110 PHE cc_start: 0.8534 (t80) cc_final: 0.8105 (t80) REVERT: E 129 THR cc_start: 0.8388 (m) cc_final: 0.7807 (p) REVERT: E 192 SER cc_start: 0.8540 (t) cc_final: 0.8274 (p) REVERT: E 200 PHE cc_start: 0.8409 (m-80) cc_final: 0.8107 (m-80) REVERT: E 211 ASP cc_start: 0.7908 (t0) cc_final: 0.7507 (t0) outliers start: 25 outliers final: 14 residues processed: 196 average time/residue: 0.7202 time to fit residues: 156.1542 Evaluate side-chains 200 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.136061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.114055 restraints weight = 12415.173| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.18 r_work: 0.3396 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 8682 Z= 0.160 Angle : 0.576 9.487 11804 Z= 0.305 Chirality : 0.043 0.222 1371 Planarity : 0.004 0.038 1486 Dihedral : 10.523 149.281 1223 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.38 % Allowed : 15.21 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.26), residues: 1098 helix: 2.50 (0.27), residues: 368 sheet: 1.07 (0.30), residues: 295 loop : -0.15 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 135 HIS 0.004 0.001 HIS B 77 PHE 0.025 0.002 PHE B 207 TYR 0.013 0.001 TYR A 324 ARG 0.006 0.001 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 446) hydrogen bonds : angle 4.65825 ( 1254) SS BOND : bond 0.00133 ( 2) SS BOND : angle 0.95673 ( 4) covalent geometry : bond 0.00370 ( 8680) covalent geometry : angle 0.57602 (11800) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.967 Fit side-chains REVERT: A 204 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.6561 (tmt) REVERT: A 241 ASN cc_start: 0.7516 (t0) cc_final: 0.7176 (t0) REVERT: A 259 VAL cc_start: 0.8285 (t) cc_final: 0.8020 (t) REVERT: A 266 VAL cc_start: 0.8195 (p) cc_final: 0.7887 (m) REVERT: A 313 VAL cc_start: 0.7526 (OUTLIER) cc_final: 0.6770 (p) REVERT: C 49 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7442 (mpt-90) REVERT: C 98 SER cc_start: 0.8355 (p) cc_final: 0.7924 (t) REVERT: C 158 VAL cc_start: 0.8485 (p) cc_final: 0.8064 (t) REVERT: C 264 TYR cc_start: 0.8485 (m-80) cc_final: 0.8249 (m-80) REVERT: C 325 MET cc_start: 0.8210 (tpp) cc_final: 0.7969 (tpt) REVERT: B 108 ASP cc_start: 0.7631 (t0) cc_final: 0.7277 (t0) REVERT: B 208 ASP cc_start: 0.8082 (m-30) cc_final: 0.7838 (m-30) REVERT: E 23 SER cc_start: 0.8234 (t) cc_final: 0.7937 (m) REVERT: E 110 PHE cc_start: 0.8587 (t80) cc_final: 0.8165 (t80) REVERT: E 192 SER cc_start: 0.8578 (t) cc_final: 0.8301 (p) REVERT: E 200 PHE cc_start: 0.8423 (m-80) cc_final: 0.8163 (m-80) REVERT: E 211 ASP cc_start: 0.7966 (t0) cc_final: 0.7540 (t0) outliers start: 21 outliers final: 12 residues processed: 191 average time/residue: 0.7357 time to fit residues: 155.0575 Evaluate side-chains 195 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 44 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 88 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.137532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115338 restraints weight = 12582.932| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.20 r_work: 0.3400 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8682 Z= 0.142 Angle : 0.567 9.491 11804 Z= 0.300 Chirality : 0.042 0.221 1371 Planarity : 0.004 0.038 1486 Dihedral : 10.444 149.166 1223 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.04 % Allowed : 15.10 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.26), residues: 1098 helix: 2.49 (0.27), residues: 368 sheet: 0.96 (0.29), residues: 301 loop : -0.14 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 135 HIS 0.004 0.001 HIS B 77 PHE 0.025 0.002 PHE B 207 TYR 0.013 0.001 TYR E 178 ARG 0.009 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 446) hydrogen bonds : angle 4.62936 ( 1254) SS BOND : bond 0.00106 ( 2) SS BOND : angle 0.82449 ( 4) covalent geometry : bond 0.00323 ( 8680) covalent geometry : angle 0.56716 (11800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6492.78 seconds wall clock time: 112 minutes 21.91 seconds (6741.91 seconds total)