Starting phenix.real_space_refine on Fri Nov 15 06:01:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/11_2024/8fn0_29302.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/11_2024/8fn0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/11_2024/8fn0_29302.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/11_2024/8fn0_29302.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/11_2024/8fn0_29302.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/11_2024/8fn0_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-5513/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: 5.46, per 1000 atoms: 0.64 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: 2.40 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: 0.97 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: 2.53 Time building geometry restraints manager: 2.63 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: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.460 Find NCS groups from input model: 0.090 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:12.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.250 ------------------------------------------------------------------------------- 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 8680 Z= 0.333 Angle : 0.948 10.266 11800 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 *********************** 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 : 0.921 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: 0.7502 time to fit residues: 184.8650 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 : 0.985 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 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 8680 Z= 0.250 Angle : 0.601 8.585 11800 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 *********************** 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 : 1.014 Fit side-chains revert: symmetry clash REVERT: A 128 PHE cc_start: 0.6820 (m-80) cc_final: 0.6573 (m-80) REVERT: A 250 MET cc_start: 0.6923 (tpp) cc_final: 0.6588 (tpt) REVERT: A 253 ILE cc_start: 0.7412 (mt) cc_final: 0.7148 (tt) REVERT: A 343 LEU cc_start: 0.7939 (tp) cc_final: 0.7624 (tt) REVERT: A 350 PHE cc_start: 0.7104 (t80) cc_final: 0.6682 (t80) REVERT: C 37 ILE cc_start: 0.8011 (mt) cc_final: 0.7613 (pt) REVERT: C 38 ASP cc_start: 0.7741 (m-30) cc_final: 0.7492 (m-30) REVERT: C 49 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7606 (mpt-90) REVERT: C 158 VAL cc_start: 0.8528 (p) cc_final: 0.8164 (t) REVERT: C 214 ARG cc_start: 0.6919 (mpt180) cc_final: 0.6335 (mpt180) REVERT: B 66 ILE cc_start: 0.8167 (mt) cc_final: 0.7935 (mm) REVERT: B 124 SER cc_start: 0.8514 (t) cc_final: 0.8237 (p) REVERT: E 17 SER cc_start: 0.8107 (p) cc_final: 0.7883 (m) REVERT: E 23 SER cc_start: 0.8248 (t) cc_final: 0.7978 (m) REVERT: E 129 THR cc_start: 0.8225 (m) cc_final: 0.7680 (p) REVERT: E 192 SER cc_start: 0.8550 (t) cc_final: 0.8288 (p) REVERT: E 211 ASP cc_start: 0.7945 (t0) cc_final: 0.7666 (t0) outliers start: 19 outliers final: 12 residues processed: 210 average time/residue: 0.7181 time to fit residues: 166.7994 Evaluate side-chains 201 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 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 55 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN C 340 ASN B 202 ASN E 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8680 Z= 0.203 Angle : 0.551 8.393 11800 Z= 0.294 Chirality : 0.043 0.261 1371 Planarity : 0.004 0.040 1486 Dihedral : 10.598 147.912 1223 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.38 % Allowed : 10.90 % 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: 1.99 (0.25), residues: 1098 helix: 2.62 (0.27), residues: 365 sheet: 1.19 (0.29), residues: 295 loop : 0.35 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 321 HIS 0.005 0.001 HIS A 325 PHE 0.016 0.002 PHE B 207 TYR 0.015 0.002 TYR E 178 ARG 0.007 0.001 ARG C 137 *********************** 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: 21 poor density : 199 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 128 PHE cc_start: 0.6878 (m-80) cc_final: 0.6658 (m-80) REVERT: A 250 MET cc_start: 0.6850 (tpp) cc_final: 0.6528 (tpt) REVERT: A 253 ILE cc_start: 0.7353 (mt) cc_final: 0.7094 (tt) REVERT: C 158 VAL cc_start: 0.8570 (p) cc_final: 0.8207 (t) REVERT: C 217 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7092 (ppp) REVERT: B 66 ILE cc_start: 0.8232 (mt) cc_final: 0.7992 (mm) REVERT: B 108 ASP cc_start: 0.7459 (t0) cc_final: 0.7193 (t0) REVERT: B 124 SER cc_start: 0.8505 (t) cc_final: 0.8251 (p) REVERT: E 17 SER cc_start: 0.8055 (p) cc_final: 0.7855 (m) REVERT: E 23 SER cc_start: 0.8241 (t) cc_final: 0.7964 (m) REVERT: E 129 THR cc_start: 0.8214 (m) cc_final: 0.7662 (p) REVERT: E 154 LEU cc_start: 0.8314 (tt) cc_final: 0.8090 (tp) REVERT: E 192 SER cc_start: 0.8493 (t) cc_final: 0.8246 (p) REVERT: E 200 PHE cc_start: 0.8530 (m-80) cc_final: 0.8199 (m-80) REVERT: E 211 ASP cc_start: 0.7886 (t0) cc_final: 0.7627 (t0) outliers start: 21 outliers final: 13 residues processed: 206 average time/residue: 0.7586 time to fit residues: 172.1818 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 : 1.026 ------------------------------------------------------------------------------- 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 252 VAL 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 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 0.0050 chunk 11 optimal weight: 0.0970 chunk 47 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 0.0670 chunk 106 optimal weight: 0.7980 chunk 52 optimal weight: 0.3980 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.2530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN E 77 ASN E 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8680 Z= 0.135 Angle : 0.516 8.327 11800 Z= 0.272 Chirality : 0.041 0.270 1371 Planarity : 0.003 0.036 1486 Dihedral : 10.417 147.816 1223 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.82 % Allowed : 12.83 % Favored : 85.36 % 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: 2.05 (0.25), residues: 1098 helix: 2.76 (0.27), residues: 365 sheet: 1.33 (0.29), residues: 289 loop : 0.24 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 135 HIS 0.002 0.001 HIS E 35 PHE 0.019 0.001 PHE A 147 TYR 0.015 0.001 TYR A 349 ARG 0.007 0.000 ARG C 137 *********************** 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 197 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 128 PHE cc_start: 0.6898 (m-80) cc_final: 0.6696 (m-80) REVERT: A 250 MET cc_start: 0.6809 (tpp) cc_final: 0.6576 (tpt) REVERT: C 158 VAL cc_start: 0.8583 (p) cc_final: 0.8219 (t) REVERT: B 66 ILE cc_start: 0.8179 (mt) cc_final: 0.7934 (mm) REVERT: B 108 ASP cc_start: 0.7478 (t0) cc_final: 0.7182 (t0) REVERT: B 208 ASP cc_start: 0.8131 (m-30) cc_final: 0.7859 (m-30) REVERT: E 23 SER cc_start: 0.8231 (t) cc_final: 0.7937 (m) REVERT: E 129 THR cc_start: 0.8205 (m) cc_final: 0.7649 (p) REVERT: E 154 LEU cc_start: 0.8310 (tt) cc_final: 0.8095 (tp) REVERT: E 192 SER cc_start: 0.8437 (t) cc_final: 0.8178 (p) REVERT: E 200 PHE cc_start: 0.8422 (m-80) cc_final: 0.8098 (m-80) REVERT: E 211 ASP cc_start: 0.7811 (t0) cc_final: 0.7561 (t0) outliers start: 16 outliers final: 8 residues processed: 184 average time/residue: 0.7828 time to fit residues: 158.5986 Evaluate side-chains 185 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 367 ILE 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 119 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 88 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 73 optimal weight: 0.0570 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 0.0050 chunk 95 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 overall best weight: 0.4912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8680 Z= 0.170 Angle : 0.532 8.698 11800 Z= 0.277 Chirality : 0.042 0.273 1371 Planarity : 0.004 0.036 1486 Dihedral : 10.380 147.921 1223 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.70 % Allowed : 14.19 % Favored : 84.11 % 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: 1.98 (0.25), residues: 1098 helix: 2.75 (0.27), residues: 367 sheet: 1.19 (0.29), residues: 291 loop : 0.20 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 135 HIS 0.004 0.001 HIS A 325 PHE 0.022 0.002 PHE A 147 TYR 0.012 0.001 TYR E 178 ARG 0.006 0.000 ARG C 137 *********************** 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 199 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 128 PHE cc_start: 0.6948 (m-80) cc_final: 0.6748 (m-80) REVERT: A 250 MET cc_start: 0.6776 (tpp) cc_final: 0.6554 (tpt) REVERT: A 259 VAL cc_start: 0.8317 (t) cc_final: 0.8061 (t) REVERT: C 101 MET cc_start: 0.8624 (mtp) cc_final: 0.8163 (mtp) REVERT: C 158 VAL cc_start: 0.8591 (p) cc_final: 0.8234 (t) REVERT: B 66 ILE cc_start: 0.8229 (mt) cc_final: 0.7965 (mm) REVERT: B 108 ASP cc_start: 0.7464 (t0) cc_final: 0.7167 (t0) REVERT: B 208 ASP cc_start: 0.8110 (m-30) cc_final: 0.7844 (m-30) REVERT: E 23 SER cc_start: 0.8245 (t) cc_final: 0.7942 (m) REVERT: E 129 THR cc_start: 0.8206 (m) cc_final: 0.7642 (p) REVERT: E 154 LEU cc_start: 0.8319 (tt) cc_final: 0.8109 (tp) REVERT: E 192 SER cc_start: 0.8446 (t) cc_final: 0.8188 (p) REVERT: E 211 ASP cc_start: 0.7839 (t0) cc_final: 0.7577 (t0) outliers start: 15 outliers final: 11 residues processed: 189 average time/residue: 0.7660 time to fit residues: 159.5510 Evaluate side-chains 190 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 179 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain C residue 61 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 119 LEU Chi-restraints excluded: chain B residue 121 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 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 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 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8680 Z= 0.250 Angle : 0.558 8.558 11800 Z= 0.296 Chirality : 0.043 0.262 1371 Planarity : 0.004 0.039 1486 Dihedral : 10.655 148.171 1223 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.82 % Allowed : 15.10 % Favored : 83.09 % 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: 1.83 (0.26), residues: 1098 helix: 2.68 (0.27), residues: 367 sheet: 1.15 (0.29), residues: 290 loop : 0.03 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 135 HIS 0.006 0.001 HIS A 325 PHE 0.020 0.002 PHE B 146 TYR 0.012 0.001 TYR E 178 ARG 0.006 0.001 ARG C 137 *********************** 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 206 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.6699 (tmt) REVERT: A 259 VAL cc_start: 0.8340 (t) cc_final: 0.8075 (t) REVERT: A 266 VAL cc_start: 0.8129 (p) cc_final: 0.7871 (m) REVERT: C 78 LYS cc_start: 0.8537 (mptp) cc_final: 0.8315 (mptt) REVERT: C 158 VAL cc_start: 0.8532 (p) cc_final: 0.8201 (t) REVERT: B 66 ILE cc_start: 0.8239 (mt) cc_final: 0.7990 (mm) REVERT: B 108 ASP cc_start: 0.7447 (t0) cc_final: 0.7127 (t0) REVERT: E 23 SER cc_start: 0.8250 (t) cc_final: 0.7947 (m) REVERT: E 129 THR cc_start: 0.8241 (m) cc_final: 0.7656 (p) REVERT: E 154 LEU cc_start: 0.8353 (tt) cc_final: 0.8143 (tp) REVERT: E 192 SER cc_start: 0.8497 (t) cc_final: 0.8255 (p) REVERT: E 211 ASP cc_start: 0.7911 (t0) cc_final: 0.7569 (t0) outliers start: 16 outliers final: 11 residues processed: 197 average time/residue: 0.7529 time to fit residues: 163.7164 Evaluate side-chains 200 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain C residue 37 ILE 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 181 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.0670 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8680 Z= 0.248 Angle : 0.558 8.913 11800 Z= 0.297 Chirality : 0.043 0.259 1371 Planarity : 0.004 0.040 1486 Dihedral : 10.761 148.305 1223 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.93 % Allowed : 14.76 % 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: 1.70 (0.26), residues: 1098 helix: 2.58 (0.27), residues: 367 sheet: 1.01 (0.29), residues: 300 loop : -0.02 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 135 HIS 0.006 0.001 HIS A 325 PHE 0.021 0.002 PHE B 146 TYR 0.012 0.001 TYR E 178 ARG 0.006 0.001 ARG F 9 *********************** 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 203 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.6737 (tmt) REVERT: A 259 VAL cc_start: 0.8347 (t) cc_final: 0.8072 (t) REVERT: C 158 VAL cc_start: 0.8600 (p) cc_final: 0.8208 (t) REVERT: B 108 ASP cc_start: 0.7441 (t0) cc_final: 0.7116 (t0) REVERT: E 23 SER cc_start: 0.8253 (t) cc_final: 0.7960 (m) REVERT: E 110 PHE cc_start: 0.8522 (t80) cc_final: 0.8063 (t80) REVERT: E 192 SER cc_start: 0.8504 (t) cc_final: 0.8255 (p) REVERT: E 211 ASP cc_start: 0.7907 (t0) cc_final: 0.7558 (t0) outliers start: 17 outliers final: 13 residues processed: 192 average time/residue: 0.7241 time to fit residues: 153.9925 Evaluate side-chains 198 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 226 THR Chi-restraints excluded: chain C residue 37 ILE 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 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 63 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8680 Z= 0.228 Angle : 0.567 9.540 11800 Z= 0.299 Chirality : 0.043 0.249 1371 Planarity : 0.004 0.039 1486 Dihedral : 10.628 148.546 1223 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.93 % Allowed : 15.21 % 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: 1.64 (0.26), residues: 1098 helix: 2.54 (0.27), residues: 367 sheet: 1.00 (0.29), residues: 300 loop : -0.09 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 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 0.001 ARG F 9 *********************** 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 210 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6670 (tmt) REVERT: A 241 ASN cc_start: 0.7573 (t0) cc_final: 0.7267 (t0) REVERT: A 259 VAL cc_start: 0.8337 (t) cc_final: 0.8062 (t) REVERT: C 98 SER cc_start: 0.8380 (p) cc_final: 0.7901 (t) REVERT: C 158 VAL cc_start: 0.8598 (p) cc_final: 0.8194 (t) REVERT: B 108 ASP cc_start: 0.7430 (t0) cc_final: 0.7099 (t0) REVERT: B 115 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.6924 (mmm) REVERT: E 23 SER cc_start: 0.8238 (t) cc_final: 0.7953 (m) REVERT: E 110 PHE cc_start: 0.8564 (t80) cc_final: 0.8120 (t80) REVERT: E 192 SER cc_start: 0.8491 (t) cc_final: 0.8240 (p) REVERT: E 211 ASP cc_start: 0.7915 (t0) cc_final: 0.7554 (t0) outliers start: 17 outliers final: 13 residues processed: 199 average time/residue: 0.7326 time to fit residues: 160.9999 Evaluate side-chains 202 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 263 THR 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 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 98 optimal weight: 0.0770 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 0.0020 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 overall best weight: 0.4946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8680 Z= 0.175 Angle : 0.541 9.358 11800 Z= 0.288 Chirality : 0.042 0.250 1371 Planarity : 0.004 0.040 1486 Dihedral : 10.482 148.648 1223 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.82 % Allowed : 15.66 % Favored : 82.52 % 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: 1.66 (0.26), residues: 1098 helix: 2.55 (0.27), residues: 368 sheet: 1.02 (0.30), residues: 299 loop : -0.09 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 135 HIS 0.004 0.001 HIS B 77 PHE 0.023 0.002 PHE B 207 TYR 0.014 0.001 TYR E 178 ARG 0.006 0.000 ARG F 9 *********************** 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 201 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 159 ASN cc_start: 0.8314 (m-40) cc_final: 0.8032 (t0) REVERT: A 204 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6598 (tmt) REVERT: A 241 ASN cc_start: 0.7551 (t0) cc_final: 0.7253 (t0) REVERT: A 259 VAL cc_start: 0.8336 (t) cc_final: 0.8066 (t) REVERT: C 98 SER cc_start: 0.8389 (p) cc_final: 0.7893 (t) REVERT: C 158 VAL cc_start: 0.8596 (p) cc_final: 0.8182 (t) REVERT: B 108 ASP cc_start: 0.7433 (t0) cc_final: 0.7093 (t0) REVERT: E 23 SER cc_start: 0.8226 (t) cc_final: 0.7941 (m) REVERT: E 110 PHE cc_start: 0.8541 (t80) cc_final: 0.8111 (t80) REVERT: E 192 SER cc_start: 0.8469 (t) cc_final: 0.8215 (p) REVERT: E 211 ASP cc_start: 0.7888 (t0) cc_final: 0.7535 (t0) outliers start: 16 outliers final: 15 residues processed: 193 average time/residue: 0.7385 time to fit residues: 157.7035 Evaluate side-chains 200 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 226 THR 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 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 172 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 49 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8680 Z= 0.242 Angle : 0.569 9.098 11800 Z= 0.302 Chirality : 0.043 0.247 1371 Planarity : 0.004 0.039 1486 Dihedral : 10.517 148.962 1223 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.93 % Allowed : 15.66 % 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: 1.56 (0.26), residues: 1098 helix: 2.46 (0.27), residues: 368 sheet: 0.97 (0.30), residues: 299 loop : -0.14 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 135 HIS 0.005 0.001 HIS B 77 PHE 0.024 0.002 PHE B 207 TYR 0.015 0.001 TYR A 324 ARG 0.005 0.001 ARG C 219 ********************** 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 208 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.900 Fit side-chains REVERT: A 159 ASN cc_start: 0.8276 (m-40) cc_final: 0.8063 (t0) REVERT: A 204 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6576 (tmt) REVERT: A 241 ASN cc_start: 0.7525 (t0) cc_final: 0.7187 (t0) REVERT: A 259 VAL cc_start: 0.8346 (t) cc_final: 0.8069 (t) REVERT: C 98 SER cc_start: 0.8384 (p) cc_final: 0.7937 (t) REVERT: C 158 VAL cc_start: 0.8601 (p) cc_final: 0.8201 (t) REVERT: B 108 ASP cc_start: 0.7425 (t0) cc_final: 0.7084 (t0) REVERT: B 208 ASP cc_start: 0.8132 (m-30) cc_final: 0.7859 (m-30) REVERT: B 211 THR cc_start: 0.8224 (m) cc_final: 0.8023 (m) REVERT: E 23 SER cc_start: 0.8243 (t) cc_final: 0.7958 (m) REVERT: E 110 PHE cc_start: 0.8562 (t80) cc_final: 0.8128 (t80) REVERT: E 192 SER cc_start: 0.8490 (t) cc_final: 0.8236 (p) REVERT: E 211 ASP cc_start: 0.7955 (t0) cc_final: 0.7574 (t0) outliers start: 17 outliers final: 14 residues processed: 198 average time/residue: 0.7086 time to fit residues: 155.9088 Evaluate side-chains 204 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 189 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 313 VAL 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 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 172 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 80 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.137518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115517 restraints weight = 12275.424| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.16 r_work: 0.3401 rms_B_bonded: 2.64 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: 0.7741 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8680 Z= 0.219 Angle : 0.560 9.417 11800 Z= 0.297 Chirality : 0.042 0.246 1371 Planarity : 0.004 0.038 1486 Dihedral : 10.495 149.067 1223 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.93 % Allowed : 16.23 % Favored : 81.84 % 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: 1.55 (0.26), residues: 1098 helix: 2.51 (0.27), residues: 367 sheet: 0.94 (0.29), residues: 299 loop : -0.19 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 135 HIS 0.005 0.001 HIS B 77 PHE 0.025 0.002 PHE B 207 TYR 0.013 0.001 TYR E 178 ARG 0.005 0.000 ARG C 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3509.41 seconds wall clock time: 63 minutes 46.30 seconds (3826.30 seconds total)