Starting phenix.real_space_refine on Mon Apr 8 05:11:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phl_13419/04_2024/7phl_13419_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phl_13419/04_2024/7phl_13419.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phl_13419/04_2024/7phl_13419_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phl_13419/04_2024/7phl_13419_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phl_13419/04_2024/7phl_13419_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phl_13419/04_2024/7phl_13419.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phl_13419/04_2024/7phl_13419.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phl_13419/04_2024/7phl_13419_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phl_13419/04_2024/7phl_13419_updated.pdb" } resolution = 3.2 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= 0.016 sd= 0.102 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 Zn 4 6.06 5 P 8 5.49 5 S 64 5.16 5 C 8272 2.51 5 N 2064 2.21 5 O 2188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ASP 41": "OD1" <-> "OD2" Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C ARG 9": "NH1" <-> "NH2" Residue "C ASP 41": "OD1" <-> "OD2" Residue "C PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C GLU 380": "OE1" <-> "OE2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ASP 41": "OD1" <-> "OD2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "D GLU 8": "OE1" <-> "OE2" Residue "D ARG 9": "NH1" <-> "NH2" Residue "D ASP 41": "OD1" <-> "OD2" Residue "D PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D GLU 242": "OE1" <-> "OE2" Residue "D TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D ARG 314": "NH1" <-> "NH2" Residue "D GLU 380": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12604 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3072 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 21, 'TRANS': 369} Chain breaks: 3 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3072 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 21, 'TRANS': 369} Chain breaks: 3 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3072 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 21, 'TRANS': 369} Chain breaks: 3 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 73 Chain: "D" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3072 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 21, 'TRANS': 369} Chain breaks: 3 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 73 Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 81 Unusual residues: {' K': 3, ' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 79 Unusual residues: {' K': 1, ' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 792 SG CYS A 104 74.670 63.686 78.914 1.00107.92 S ATOM 798 SG CYS A 105 72.228 65.678 80.070 1.00105.62 S ATOM 6767 SG CYS B 83 70.601 63.013 80.849 1.00103.76 S ATOM 3864 SG CYS C 104 46.202 57.222 78.998 1.00107.92 S ATOM 3870 SG CYS C 105 48.649 55.233 80.149 1.00105.62 S ATOM 9839 SG CYS D 83 50.455 57.919 80.857 1.00103.76 S ATOM 3695 SG CYS C 83 63.008 50.358 80.885 1.00103.76 S ATOM 6936 SG CYS B 104 63.643 46.243 78.983 1.00107.92 S ATOM 6942 SG CYS B 105 65.647 48.680 80.131 1.00105.62 S ATOM 623 SG CYS A 83 57.881 70.585 80.826 1.00103.76 S ATOM 10008 SG CYS D 104 57.376 74.699 78.944 1.00107.92 S ATOM 10014 SG CYS D 105 55.379 72.260 80.100 1.00105.62 S Time building chain proxies: 6.47, per 1000 atoms: 0.51 Number of scatterers: 12604 At special positions: 0 Unit cell: (121.8, 121.8, 123.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 K 4 19.00 S 64 16.00 P 8 15.00 O 2188 8.00 N 2064 7.00 C 8272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.87 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" ND1 HIS A 77 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 104 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 105 " pdb="ZN ZN A 603 " - pdb=" SG CYS B 83 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 77 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 104 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 105 " pdb="ZN ZN B 601 " - pdb=" SG CYS C 83 " pdb=" ZN C 603 " pdb="ZN ZN C 603 " - pdb=" ND1 HIS C 77 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 105 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 104 " pdb="ZN ZN C 603 " - pdb=" SG CYS D 83 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 77 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 105 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 104 " pdb="ZN ZN D 601 " - pdb=" SG CYS A 83 " Number of angles added : 12 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 4 sheets defined 65.5% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 42 through 45 No H-bonds generated for 'chain 'A' and resid 42 through 45' Processing helix chain 'A' and resid 61 through 73 removed outlier: 4.555A pdb=" N HIS A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 94 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 103 through 109 removed outlier: 4.524A pdb=" N MET A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N THR A 108 " --> pdb=" O CYS A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 119 Processing helix chain 'A' and resid 173 through 179 removed outlier: 4.263A pdb=" N LEU A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 187 through 210 Processing helix chain 'A' and resid 243 through 265 Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 277 through 294 Proline residue: A 288 - end of helix removed outlier: 3.724A pdb=" N GLU A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL A 293 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY A 294 " --> pdb=" O TYR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 327 removed outlier: 3.853A pdb=" N ASP A 305 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL A 316 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N PHE A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N HIS A 327 " --> pdb=" O LYS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 340 Processing helix chain 'A' and resid 342 through 368 removed outlier: 3.722A pdb=" N ARG A 368 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 Processing helix chain 'A' and resid 411 through 429 Processing helix chain 'A' and resid 432 through 451 Processing helix chain 'C' and resid 23 through 28 Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'C' and resid 42 through 45 No H-bonds generated for 'chain 'C' and resid 42 through 45' Processing helix chain 'C' and resid 61 through 73 removed outlier: 4.555A pdb=" N HIS C 66 " --> pdb=" O GLY C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 103 through 109 removed outlier: 4.524A pdb=" N MET C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N THR C 108 " --> pdb=" O CYS C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 119 Processing helix chain 'C' and resid 173 through 179 removed outlier: 4.264A pdb=" N LEU C 179 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 187 through 210 Processing helix chain 'C' and resid 243 through 265 Processing helix chain 'C' and resid 270 through 275 Processing helix chain 'C' and resid 277 through 294 Proline residue: C 288 - end of helix removed outlier: 3.724A pdb=" N GLU C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL C 293 " --> pdb=" O PHE C 289 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY C 294 " --> pdb=" O TYR C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 327 removed outlier: 3.853A pdb=" N ASP C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL C 316 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE C 318 " --> pdb=" O ARG C 314 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG C 320 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE C 321 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N PHE C 322 " --> pdb=" O ILE C 318 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N HIS C 327 " --> pdb=" O LYS C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 340 Processing helix chain 'C' and resid 342 through 368 removed outlier: 3.723A pdb=" N ARG C 368 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 398 Processing helix chain 'C' and resid 411 through 429 Processing helix chain 'C' and resid 432 through 451 Processing helix chain 'B' and resid 23 through 28 Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 42 through 45 No H-bonds generated for 'chain 'B' and resid 42 through 45' Processing helix chain 'B' and resid 61 through 73 removed outlier: 4.555A pdb=" N HIS B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 103 through 109 removed outlier: 4.524A pdb=" N MET B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N THR B 108 " --> pdb=" O CYS B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 119 Processing helix chain 'B' and resid 173 through 179 removed outlier: 4.264A pdb=" N LEU B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 187 through 210 Processing helix chain 'B' and resid 243 through 265 Processing helix chain 'B' and resid 270 through 275 Processing helix chain 'B' and resid 277 through 294 Proline residue: B 288 - end of helix removed outlier: 3.724A pdb=" N GLU B 292 " --> pdb=" O PRO B 288 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY B 294 " --> pdb=" O TYR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 327 removed outlier: 3.853A pdb=" N ASP B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL B 316 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE B 318 " --> pdb=" O ARG B 314 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG B 320 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N PHE B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N HIS B 327 " --> pdb=" O LYS B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 340 Processing helix chain 'B' and resid 342 through 368 removed outlier: 3.722A pdb=" N ARG B 368 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 398 Processing helix chain 'B' and resid 411 through 429 Processing helix chain 'B' and resid 432 through 451 Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 33 through 38 Processing helix chain 'D' and resid 42 through 45 No H-bonds generated for 'chain 'D' and resid 42 through 45' Processing helix chain 'D' and resid 61 through 73 removed outlier: 4.554A pdb=" N HIS D 66 " --> pdb=" O GLY D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 94 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 103 through 109 removed outlier: 4.525A pdb=" N MET D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N THR D 108 " --> pdb=" O CYS D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 173 through 179 removed outlier: 4.264A pdb=" N LEU D 179 " --> pdb=" O ARG D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 187 through 210 Processing helix chain 'D' and resid 243 through 265 Processing helix chain 'D' and resid 270 through 275 Processing helix chain 'D' and resid 277 through 294 Proline residue: D 288 - end of helix removed outlier: 3.725A pdb=" N GLU D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL D 293 " --> pdb=" O PHE D 289 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY D 294 " --> pdb=" O TYR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 327 removed outlier: 3.852A pdb=" N ASP D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL D 316 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG D 317 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE D 318 " --> pdb=" O ARG D 314 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG D 320 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE D 321 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N PHE D 322 " --> pdb=" O ILE D 318 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N HIS D 327 " --> pdb=" O LYS D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 340 Processing helix chain 'D' and resid 342 through 368 removed outlier: 3.722A pdb=" N ARG D 368 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 398 Processing helix chain 'D' and resid 411 through 429 Processing helix chain 'D' and resid 432 through 451 Processing sheet with id= A, first strand: chain 'A' and resid 17 through 22 Processing sheet with id= B, first strand: chain 'C' and resid 17 through 22 Processing sheet with id= C, first strand: chain 'B' and resid 17 through 22 Processing sheet with id= D, first strand: chain 'D' and resid 17 through 22 656 hydrogen bonds defined for protein. 1956 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.73 Time building geometry restraints manager: 5.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1928 1.31 - 1.43: 3780 1.43 - 1.56: 7129 1.56 - 1.69: 19 1.69 - 1.81: 96 Bond restraints: 12952 Sorted by residual: bond pdb=" CG LEU B 401 " pdb=" CD1 LEU B 401 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.57e+00 bond pdb=" CG LEU A 401 " pdb=" CD1 LEU A 401 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" CG LEU C 401 " pdb=" CD1 LEU C 401 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.53e+00 bond pdb=" CG LEU D 401 " pdb=" CD1 LEU D 401 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.47e+00 bond pdb=" N PCF B 603 " pdb=" C12 PCF B 603 " ideal model delta sigma weight residual 1.447 1.477 -0.030 2.00e-02 2.50e+03 2.21e+00 ... (remaining 12947 not shown) Histogram of bond angle deviations from ideal: 99.29 - 106.25: 393 106.25 - 113.21: 7062 113.21 - 120.18: 4809 120.18 - 127.14: 5157 127.14 - 134.10: 207 Bond angle restraints: 17628 Sorted by residual: angle pdb=" CA LEU B 91 " pdb=" CB LEU B 91 " pdb=" CG LEU B 91 " ideal model delta sigma weight residual 116.30 124.55 -8.25 3.50e+00 8.16e-02 5.56e+00 angle pdb=" CA LEU A 91 " pdb=" CB LEU A 91 " pdb=" CG LEU A 91 " ideal model delta sigma weight residual 116.30 124.54 -8.24 3.50e+00 8.16e-02 5.54e+00 angle pdb=" CA LEU D 91 " pdb=" CB LEU D 91 " pdb=" CG LEU D 91 " ideal model delta sigma weight residual 116.30 124.52 -8.22 3.50e+00 8.16e-02 5.52e+00 angle pdb=" CA LEU C 91 " pdb=" CB LEU C 91 " pdb=" CG LEU C 91 " ideal model delta sigma weight residual 116.30 124.51 -8.21 3.50e+00 8.16e-02 5.50e+00 angle pdb=" C11 PCF A 602 " pdb=" O13 PCF A 602 " pdb=" P PCF A 602 " ideal model delta sigma weight residual 118.48 124.00 -5.52 3.00e+00 1.11e-01 3.38e+00 ... (remaining 17623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 6861 17.73 - 35.46: 451 35.46 - 53.19: 136 53.19 - 70.91: 32 70.91 - 88.64: 16 Dihedral angle restraints: 7496 sinusoidal: 2928 harmonic: 4568 Sorted by residual: dihedral pdb=" CG ARG C 9 " pdb=" CD ARG C 9 " pdb=" NE ARG C 9 " pdb=" CZ ARG C 9 " ideal model delta sinusoidal sigma weight residual -180.00 -135.55 -44.45 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG B 9 " pdb=" CD ARG B 9 " pdb=" NE ARG B 9 " pdb=" CZ ARG B 9 " ideal model delta sinusoidal sigma weight residual -180.00 -135.56 -44.44 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG A 9 " pdb=" CD ARG A 9 " pdb=" NE ARG A 9 " pdb=" CZ ARG A 9 " ideal model delta sinusoidal sigma weight residual -180.00 -135.57 -44.43 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 7493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 973 0.030 - 0.059: 592 0.059 - 0.089: 265 0.089 - 0.119: 78 0.119 - 0.148: 36 Chirality restraints: 1944 Sorted by residual: chirality pdb=" CA PRO D 40 " pdb=" N PRO D 40 " pdb=" C PRO D 40 " pdb=" CB PRO D 40 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA PRO C 40 " pdb=" N PRO C 40 " pdb=" C PRO C 40 " pdb=" CB PRO C 40 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA PRO A 40 " pdb=" N PRO A 40 " pdb=" C PRO A 40 " pdb=" CB PRO A 40 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 1941 not shown) Planarity restraints: 2204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 84 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO C 85 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 85 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 85 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 84 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO A 85 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 84 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO D 85 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 85 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 85 " 0.030 5.00e-02 4.00e+02 ... (remaining 2201 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.96: 6201 2.96 - 3.51: 14839 3.51 - 4.05: 21507 4.05 - 4.60: 33608 4.60 - 5.14: 45474 Nonbonded interactions: 121629 Sorted by model distance: nonbonded pdb=" NH1 ARG C 33 " pdb=" O PHE C 93 " model vdw 2.418 2.520 nonbonded pdb=" NH1 ARG D 33 " pdb=" O PHE D 93 " model vdw 2.419 2.520 nonbonded pdb=" NH1 ARG A 33 " pdb=" O PHE A 93 " model vdw 2.419 2.520 nonbonded pdb=" NH1 ARG B 33 " pdb=" O PHE B 93 " model vdw 2.419 2.520 nonbonded pdb=" NH1 ARG B 263 " pdb=" OD1 ASN B 279 " model vdw 2.424 2.520 ... (remaining 121624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 463 or resid 602)) selection = (chain 'B' and (resid 7 through 463 or (resid 602 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C3 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or na \ me O31 or name O32 or name P )))) selection = (chain 'C' and (resid 7 through 463 or resid 602)) selection = (chain 'D' and (resid 7 through 463 or (resid 602 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C3 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or na \ me O31 or name O32 or name P )))) } 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.300 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 38.340 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 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 : 0.007 0.053 12952 Z= 0.471 Angle : 0.683 8.255 17628 Z= 0.371 Chirality : 0.046 0.148 1944 Planarity : 0.006 0.055 2204 Dihedral : 14.471 88.643 4536 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.96 % Allowed : 4.81 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.03 (0.19), residues: 1532 helix: -0.31 (0.15), residues: 960 sheet: -0.26 (0.72), residues: 40 loop : -1.18 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 411 HIS 0.009 0.002 HIS B 212 PHE 0.015 0.002 PHE A 207 TYR 0.019 0.002 TYR A 109 ARG 0.010 0.001 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 196 time to evaluate : 1.480 Fit side-chains REVERT: A 36 TRP cc_start: 0.6584 (m-10) cc_final: 0.6300 (m-10) REVERT: A 54 GLU cc_start: 0.7785 (pt0) cc_final: 0.7580 (pt0) REVERT: A 107 MET cc_start: 0.8011 (mmp) cc_final: 0.6309 (mpp) REVERT: A 177 TRP cc_start: 0.5229 (t-100) cc_final: 0.5023 (t-100) REVERT: A 213 GLU cc_start: 0.7149 (tt0) cc_final: 0.6792 (tp30) REVERT: A 242 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6939 (mt-10) REVERT: A 263 ARG cc_start: 0.5545 (OUTLIER) cc_final: 0.4746 (mtp-110) REVERT: A 406 MET cc_start: 0.8414 (ptp) cc_final: 0.7951 (ptp) REVERT: A 449 LYS cc_start: 0.6875 (mttt) cc_final: 0.6667 (mttp) REVERT: C 48 TYR cc_start: 0.8143 (t80) cc_final: 0.7566 (t80) REVERT: C 81 ASP cc_start: 0.7308 (p0) cc_final: 0.7072 (p0) REVERT: C 213 GLU cc_start: 0.7183 (tt0) cc_final: 0.6903 (tp30) REVERT: C 242 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6988 (mt-10) REVERT: C 406 MET cc_start: 0.8467 (ptp) cc_final: 0.8224 (ptp) REVERT: C 449 LYS cc_start: 0.6793 (mttt) cc_final: 0.6561 (mttp) REVERT: B 36 TRP cc_start: 0.6676 (m-10) cc_final: 0.6413 (m-10) REVERT: B 107 MET cc_start: 0.7953 (mmp) cc_final: 0.6481 (mpp) REVERT: B 213 GLU cc_start: 0.7100 (tt0) cc_final: 0.6782 (tp30) REVERT: B 244 PHE cc_start: 0.5383 (m-80) cc_final: 0.5058 (m-80) REVERT: B 247 TYR cc_start: 0.6270 (m-80) cc_final: 0.5743 (m-10) REVERT: D 36 TRP cc_start: 0.6606 (m-10) cc_final: 0.6253 (m-10) REVERT: D 107 MET cc_start: 0.7921 (mmp) cc_final: 0.6410 (mpp) REVERT: D 213 GLU cc_start: 0.7204 (tt0) cc_final: 0.6908 (tp30) REVERT: D 242 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6993 (mt-10) REVERT: D 263 ARG cc_start: 0.5572 (OUTLIER) cc_final: 0.4953 (mtp-110) REVERT: D 290 TYR cc_start: 0.4431 (OUTLIER) cc_final: 0.4143 (m-80) REVERT: D 449 LYS cc_start: 0.6820 (mttt) cc_final: 0.6564 (mttp) outliers start: 12 outliers final: 0 residues processed: 204 average time/residue: 0.2957 time to fit residues: 84.5911 Evaluate side-chains 172 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 169 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 290 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 91 optimal weight: 20.0000 chunk 141 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN C 111 GLN C 279 ASN B 111 GLN D 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12952 Z= 0.223 Angle : 0.511 8.409 17628 Z= 0.256 Chirality : 0.040 0.240 1944 Planarity : 0.004 0.049 2204 Dihedral : 9.343 59.840 1898 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.28 % Allowed : 8.25 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.06 (0.21), residues: 1532 helix: 1.41 (0.17), residues: 928 sheet: None (None), residues: 0 loop : -0.35 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 177 HIS 0.003 0.001 HIS C 77 PHE 0.019 0.001 PHE A 199 TYR 0.015 0.001 TYR A 290 ARG 0.002 0.000 ARG D 320 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 171 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.5650 (OUTLIER) cc_final: 0.5183 (mp) REVERT: A 213 GLU cc_start: 0.7227 (tt0) cc_final: 0.6845 (tp30) REVERT: A 242 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6925 (mt-10) REVERT: A 458 LYS cc_start: 0.7169 (mtmm) cc_final: 0.6933 (mttp) REVERT: C 48 TYR cc_start: 0.7971 (t80) cc_final: 0.7616 (t80) REVERT: C 67 ILE cc_start: 0.5668 (OUTLIER) cc_final: 0.5201 (mp) REVERT: C 81 ASP cc_start: 0.7531 (p0) cc_final: 0.7289 (p0) REVERT: C 107 MET cc_start: 0.7832 (mmp) cc_final: 0.6121 (mpp) REVERT: C 177 TRP cc_start: 0.5638 (t-100) cc_final: 0.5401 (t-100) REVERT: C 213 GLU cc_start: 0.7172 (tt0) cc_final: 0.6836 (tp30) REVERT: C 242 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6930 (mt-10) REVERT: B 48 TYR cc_start: 0.8142 (t80) cc_final: 0.7798 (t80) REVERT: B 67 ILE cc_start: 0.5678 (OUTLIER) cc_final: 0.5214 (mp) REVERT: B 107 MET cc_start: 0.7751 (mmp) cc_final: 0.6208 (mpp) REVERT: D 53 ASP cc_start: 0.7462 (t70) cc_final: 0.7162 (t0) REVERT: D 67 ILE cc_start: 0.5655 (OUTLIER) cc_final: 0.5194 (mp) REVERT: D 107 MET cc_start: 0.7784 (mmp) cc_final: 0.6223 (mpp) REVERT: D 213 GLU cc_start: 0.7242 (tt0) cc_final: 0.7030 (tp30) REVERT: D 242 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6930 (mt-10) outliers start: 16 outliers final: 6 residues processed: 182 average time/residue: 0.2400 time to fit residues: 64.4654 Evaluate side-chains 167 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 157 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 389 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS C 22 HIS B 22 HIS D 22 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12952 Z= 0.356 Angle : 0.557 9.151 17628 Z= 0.279 Chirality : 0.044 0.303 1944 Planarity : 0.005 0.055 2204 Dihedral : 8.963 58.894 1888 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.00 % Allowed : 9.86 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.21), residues: 1532 helix: 1.07 (0.16), residues: 1000 sheet: None (None), residues: 0 loop : -0.45 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 177 HIS 0.007 0.001 HIS B 77 PHE 0.018 0.002 PHE D 289 TYR 0.024 0.002 TYR A 48 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.5811 (OUTLIER) cc_final: 0.5354 (mp) REVERT: A 213 GLU cc_start: 0.7253 (tt0) cc_final: 0.6812 (tp30) REVERT: A 242 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6985 (mt-10) REVERT: A 458 LYS cc_start: 0.7224 (mtmm) cc_final: 0.6966 (mttp) REVERT: C 48 TYR cc_start: 0.8008 (t80) cc_final: 0.7716 (t80) REVERT: C 67 ILE cc_start: 0.5759 (OUTLIER) cc_final: 0.5301 (mp) REVERT: C 81 ASP cc_start: 0.7755 (p0) cc_final: 0.7555 (p0) REVERT: C 107 MET cc_start: 0.7772 (mmp) cc_final: 0.6055 (mpp) REVERT: C 213 GLU cc_start: 0.7272 (tt0) cc_final: 0.6901 (tp30) REVERT: C 242 GLU cc_start: 0.7296 (mt-10) cc_final: 0.7012 (mt-10) REVERT: B 48 TYR cc_start: 0.8180 (t80) cc_final: 0.7859 (t80) REVERT: B 67 ILE cc_start: 0.5827 (OUTLIER) cc_final: 0.5357 (mp) REVERT: B 107 MET cc_start: 0.7703 (mmp) cc_final: 0.6111 (mpp) REVERT: B 242 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6887 (mt-10) REVERT: B 458 LYS cc_start: 0.6928 (mttp) cc_final: 0.6650 (mttp) REVERT: D 53 ASP cc_start: 0.7564 (t70) cc_final: 0.7278 (t0) REVERT: D 67 ILE cc_start: 0.5824 (OUTLIER) cc_final: 0.5356 (mp) REVERT: D 107 MET cc_start: 0.7705 (mmp) cc_final: 0.6095 (mpp) REVERT: D 213 GLU cc_start: 0.7367 (tt0) cc_final: 0.7072 (tp30) REVERT: D 242 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6977 (mt-10) outliers start: 25 outliers final: 21 residues processed: 165 average time/residue: 0.2093 time to fit residues: 52.4256 Evaluate side-chains 160 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 389 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 95 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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: 0.6406 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12952 Z= 0.311 Angle : 0.524 8.770 17628 Z= 0.262 Chirality : 0.043 0.316 1944 Planarity : 0.005 0.054 2204 Dihedral : 8.507 59.899 1888 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.32 % Allowed : 11.54 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.21), residues: 1532 helix: 1.13 (0.17), residues: 1000 sheet: None (None), residues: 0 loop : -0.41 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 177 HIS 0.005 0.001 HIS B 77 PHE 0.013 0.001 PHE B 315 TYR 0.027 0.002 TYR A 48 ARG 0.002 0.000 ARG C 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8291 (t80) cc_final: 0.7947 (t80) REVERT: A 67 ILE cc_start: 0.5763 (OUTLIER) cc_final: 0.5299 (mp) REVERT: A 111 GLN cc_start: 0.7588 (tt0) cc_final: 0.7295 (tt0) REVERT: A 177 TRP cc_start: 0.5390 (t-100) cc_final: 0.4283 (m-90) REVERT: A 213 GLU cc_start: 0.7334 (tt0) cc_final: 0.6811 (tp30) REVERT: A 242 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6980 (mt-10) REVERT: A 458 LYS cc_start: 0.7199 (mtmm) cc_final: 0.6945 (mttp) REVERT: C 48 TYR cc_start: 0.8000 (t80) cc_final: 0.7635 (t80) REVERT: C 67 ILE cc_start: 0.5739 (OUTLIER) cc_final: 0.5265 (mp) REVERT: C 107 MET cc_start: 0.7767 (mmp) cc_final: 0.6080 (mpp) REVERT: C 177 TRP cc_start: 0.5422 (t-100) cc_final: 0.4463 (m-90) REVERT: C 213 GLU cc_start: 0.7310 (tt0) cc_final: 0.6954 (tp30) REVERT: C 242 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6904 (mt-10) REVERT: B 48 TYR cc_start: 0.8237 (t80) cc_final: 0.7976 (t80) REVERT: B 53 ASP cc_start: 0.7604 (t70) cc_final: 0.7384 (t0) REVERT: B 67 ILE cc_start: 0.5745 (OUTLIER) cc_final: 0.5272 (mp) REVERT: B 107 MET cc_start: 0.7658 (mmp) cc_final: 0.6103 (mpp) REVERT: B 210 GLU cc_start: 0.5989 (tt0) cc_final: 0.5481 (mt-10) REVERT: B 242 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6796 (mt-10) REVERT: D 53 ASP cc_start: 0.7626 (t70) cc_final: 0.7190 (t0) REVERT: D 67 ILE cc_start: 0.5732 (OUTLIER) cc_final: 0.5264 (mp) REVERT: D 107 MET cc_start: 0.7667 (mmp) cc_final: 0.6098 (mpp) REVERT: D 213 GLU cc_start: 0.7385 (tt0) cc_final: 0.7037 (tp30) REVERT: D 242 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6855 (mt-10) outliers start: 29 outliers final: 16 residues processed: 167 average time/residue: 0.2171 time to fit residues: 55.0412 Evaluate side-chains 154 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 389 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 2.9990 chunk 85 optimal weight: 0.0870 chunk 2 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 overall best weight: 2.6166 ------------------------------------------------------------------------------- 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: 0.6438 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12952 Z= 0.414 Angle : 0.572 8.904 17628 Z= 0.289 Chirality : 0.045 0.317 1944 Planarity : 0.005 0.057 2204 Dihedral : 8.519 58.835 1888 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.88 % Allowed : 11.38 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1532 helix: 0.89 (0.16), residues: 1004 sheet: None (None), residues: 0 loop : -0.64 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 392 HIS 0.007 0.001 HIS A 77 PHE 0.013 0.002 PHE C 315 TYR 0.023 0.002 TYR A 48 ARG 0.003 0.000 ARG C 320 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 127 time to evaluate : 1.327 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7739 (t70) cc_final: 0.7464 (t0) REVERT: A 54 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7381 (pt0) REVERT: A 67 ILE cc_start: 0.5887 (OUTLIER) cc_final: 0.5445 (mp) REVERT: A 177 TRP cc_start: 0.5199 (t-100) cc_final: 0.4126 (m-90) REVERT: A 213 GLU cc_start: 0.7406 (tt0) cc_final: 0.6803 (tp30) REVERT: A 242 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6910 (mt-10) REVERT: A 458 LYS cc_start: 0.7278 (mtmm) cc_final: 0.6994 (mttp) REVERT: C 48 TYR cc_start: 0.8040 (t80) cc_final: 0.7764 (t80) REVERT: C 67 ILE cc_start: 0.5880 (OUTLIER) cc_final: 0.5436 (mp) REVERT: C 107 MET cc_start: 0.7725 (mmp) cc_final: 0.6053 (mpp) REVERT: C 177 TRP cc_start: 0.5238 (t-100) cc_final: 0.4302 (m-90) REVERT: C 213 GLU cc_start: 0.7391 (tt0) cc_final: 0.6815 (tp30) REVERT: C 242 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6910 (mt-10) REVERT: B 48 TYR cc_start: 0.8284 (t80) cc_final: 0.7793 (t80) REVERT: B 53 ASP cc_start: 0.7673 (t70) cc_final: 0.7351 (t0) REVERT: B 67 ILE cc_start: 0.5879 (OUTLIER) cc_final: 0.5409 (mp) REVERT: B 107 MET cc_start: 0.7608 (mmp) cc_final: 0.6037 (mpp) REVERT: B 210 GLU cc_start: 0.6007 (tt0) cc_final: 0.5511 (mt-10) REVERT: B 242 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6831 (mt-10) REVERT: D 53 ASP cc_start: 0.7732 (t70) cc_final: 0.7456 (t0) REVERT: D 67 ILE cc_start: 0.5862 (OUTLIER) cc_final: 0.5417 (mp) REVERT: D 107 MET cc_start: 0.7617 (mmp) cc_final: 0.6025 (mpp) REVERT: D 213 GLU cc_start: 0.7394 (tt0) cc_final: 0.6831 (tp30) REVERT: D 242 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6862 (mt-10) outliers start: 36 outliers final: 24 residues processed: 160 average time/residue: 0.2106 time to fit residues: 51.0493 Evaluate side-chains 153 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 124 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 105 CYS Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 396 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 20.0000 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.6368 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12952 Z= 0.178 Angle : 0.465 8.522 17628 Z= 0.232 Chirality : 0.040 0.265 1944 Planarity : 0.005 0.047 2204 Dihedral : 7.682 59.602 1888 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.08 % Allowed : 12.82 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.21), residues: 1532 helix: 1.24 (0.17), residues: 1004 sheet: None (None), residues: 0 loop : -0.25 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 94 HIS 0.002 0.001 HIS C 112 PHE 0.011 0.001 PHE A 199 TYR 0.026 0.001 TYR A 48 ARG 0.002 0.000 ARG C 320 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 1.349 Fit side-chains revert: symmetry clash REVERT: A 54 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7591 (pt0) REVERT: A 67 ILE cc_start: 0.5721 (OUTLIER) cc_final: 0.5268 (mp) REVERT: A 177 TRP cc_start: 0.5254 (t-100) cc_final: 0.4333 (m-90) REVERT: A 213 GLU cc_start: 0.7339 (tt0) cc_final: 0.6783 (tp30) REVERT: A 242 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6937 (mt-10) REVERT: A 458 LYS cc_start: 0.7199 (mtmm) cc_final: 0.6996 (mttp) REVERT: C 48 TYR cc_start: 0.7867 (t80) cc_final: 0.7491 (t80) REVERT: C 67 ILE cc_start: 0.5709 (OUTLIER) cc_final: 0.5252 (mp) REVERT: C 107 MET cc_start: 0.7660 (mmp) cc_final: 0.6033 (mpp) REVERT: C 117 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6166 (pp20) REVERT: C 177 TRP cc_start: 0.5270 (t-100) cc_final: 0.4328 (m-90) REVERT: C 210 GLU cc_start: 0.5966 (tt0) cc_final: 0.5373 (mt-10) REVERT: C 213 GLU cc_start: 0.7354 (tt0) cc_final: 0.6962 (tp30) REVERT: C 242 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6908 (mt-10) REVERT: B 53 ASP cc_start: 0.7719 (t70) cc_final: 0.7395 (t0) REVERT: B 67 ILE cc_start: 0.5708 (OUTLIER) cc_final: 0.5251 (mp) REVERT: B 107 MET cc_start: 0.7512 (mmp) cc_final: 0.6020 (mpp) REVERT: B 210 GLU cc_start: 0.5983 (tt0) cc_final: 0.5364 (mt-10) REVERT: B 242 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6861 (mt-10) REVERT: D 67 ILE cc_start: 0.5696 (OUTLIER) cc_final: 0.5243 (mp) REVERT: D 107 MET cc_start: 0.7532 (mmp) cc_final: 0.6010 (mpp) REVERT: D 210 GLU cc_start: 0.6035 (tt0) cc_final: 0.5501 (mt-10) REVERT: D 213 GLU cc_start: 0.7355 (tt0) cc_final: 0.6821 (tp30) REVERT: D 242 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6911 (mt-10) outliers start: 26 outliers final: 12 residues processed: 167 average time/residue: 0.2234 time to fit residues: 56.6643 Evaluate side-chains 157 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 389 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 0.0570 chunk 110 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 69 optimal weight: 0.0010 chunk 93 optimal weight: 2.9990 overall best weight: 0.7506 ------------------------------------------------------------------------------- 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: 0.6360 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12952 Z= 0.174 Angle : 0.455 8.289 17628 Z= 0.227 Chirality : 0.039 0.239 1944 Planarity : 0.005 0.045 2204 Dihedral : 7.193 59.849 1888 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.84 % Allowed : 13.62 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.31 (0.22), residues: 1532 helix: 1.42 (0.17), residues: 1004 sheet: None (None), residues: 0 loop : -0.08 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 177 HIS 0.002 0.001 HIS D 112 PHE 0.022 0.001 PHE B 93 TYR 0.022 0.001 TYR A 48 ARG 0.002 0.000 ARG C 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.5723 (OUTLIER) cc_final: 0.5292 (mp) REVERT: A 107 MET cc_start: 0.7476 (mmp) cc_final: 0.5970 (mpp) REVERT: A 177 TRP cc_start: 0.5343 (t-100) cc_final: 0.4488 (m-90) REVERT: A 210 GLU cc_start: 0.5974 (tt0) cc_final: 0.5502 (mt-10) REVERT: A 213 GLU cc_start: 0.7349 (tt0) cc_final: 0.6814 (tp30) REVERT: A 242 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6970 (mt-10) REVERT: C 48 TYR cc_start: 0.7793 (t80) cc_final: 0.7368 (t80) REVERT: C 67 ILE cc_start: 0.5693 (OUTLIER) cc_final: 0.5256 (mp) REVERT: C 107 MET cc_start: 0.7601 (mmp) cc_final: 0.6005 (mpp) REVERT: C 117 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6207 (pp20) REVERT: C 177 TRP cc_start: 0.5344 (t-100) cc_final: 0.4528 (m-90) REVERT: C 210 GLU cc_start: 0.5979 (tt0) cc_final: 0.5445 (mt-10) REVERT: C 213 GLU cc_start: 0.7360 (tt0) cc_final: 0.6687 (mp0) REVERT: C 242 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6933 (mt-10) REVERT: B 67 ILE cc_start: 0.5692 (OUTLIER) cc_final: 0.5231 (mp) REVERT: B 107 MET cc_start: 0.7505 (mmp) cc_final: 0.6027 (mpp) REVERT: B 210 GLU cc_start: 0.5974 (tt0) cc_final: 0.5359 (mt-10) REVERT: B 242 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6865 (mt-10) REVERT: D 67 ILE cc_start: 0.5682 (OUTLIER) cc_final: 0.5244 (mp) REVERT: D 107 MET cc_start: 0.7519 (mmp) cc_final: 0.5994 (mpp) REVERT: D 177 TRP cc_start: 0.5459 (t-100) cc_final: 0.4526 (m-90) REVERT: D 210 GLU cc_start: 0.6050 (tt0) cc_final: 0.5514 (mt-10) REVERT: D 213 GLU cc_start: 0.7368 (tt0) cc_final: 0.7015 (tp30) REVERT: D 242 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6900 (mt-10) REVERT: D 458 LYS cc_start: 0.6915 (mttp) cc_final: 0.6649 (mttp) outliers start: 23 outliers final: 14 residues processed: 159 average time/residue: 0.2400 time to fit residues: 57.7636 Evaluate side-chains 153 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 389 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 102 optimal weight: 0.3980 chunk 74 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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: 0.6419 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12952 Z= 0.339 Angle : 0.526 8.246 17628 Z= 0.265 Chirality : 0.043 0.313 1944 Planarity : 0.005 0.051 2204 Dihedral : 7.662 59.514 1888 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.08 % Allowed : 13.30 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.21 (0.22), residues: 1532 helix: 1.30 (0.17), residues: 984 sheet: None (None), residues: 0 loop : 0.02 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 392 HIS 0.006 0.001 HIS A 77 PHE 0.018 0.001 PHE D 93 TYR 0.021 0.002 TYR A 48 ARG 0.003 0.000 ARG C 320 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 1.375 Fit side-chains revert: symmetry clash REVERT: A 67 ILE cc_start: 0.5833 (OUTLIER) cc_final: 0.5392 (mp) REVERT: A 107 MET cc_start: 0.7546 (mmp) cc_final: 0.6010 (mpp) REVERT: A 177 TRP cc_start: 0.5184 (t-100) cc_final: 0.4332 (m-90) REVERT: A 210 GLU cc_start: 0.6015 (tt0) cc_final: 0.5532 (mt-10) REVERT: A 213 GLU cc_start: 0.7403 (tt0) cc_final: 0.6794 (tp30) REVERT: A 242 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6931 (mt-10) REVERT: A 458 LYS cc_start: 0.7228 (mtmm) cc_final: 0.6982 (mttp) REVERT: C 48 TYR cc_start: 0.7868 (t80) cc_final: 0.7512 (t80) REVERT: C 67 ILE cc_start: 0.5834 (OUTLIER) cc_final: 0.5363 (mp) REVERT: C 107 MET cc_start: 0.7673 (mmp) cc_final: 0.6045 (mpp) REVERT: C 177 TRP cc_start: 0.5297 (t-100) cc_final: 0.4513 (m-90) REVERT: C 213 GLU cc_start: 0.7405 (tt0) cc_final: 0.6721 (mp0) REVERT: C 242 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6941 (mt-10) REVERT: B 67 ILE cc_start: 0.5825 (OUTLIER) cc_final: 0.5359 (mp) REVERT: B 107 MET cc_start: 0.7553 (mmp) cc_final: 0.6048 (mpp) REVERT: B 210 GLU cc_start: 0.6028 (tt0) cc_final: 0.5538 (mt-10) REVERT: B 242 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6834 (mt-10) REVERT: D 67 ILE cc_start: 0.5783 (OUTLIER) cc_final: 0.5313 (mp) REVERT: D 107 MET cc_start: 0.7575 (mmp) cc_final: 0.6001 (mpp) REVERT: D 177 TRP cc_start: 0.5426 (t-100) cc_final: 0.4810 (m-90) REVERT: D 210 GLU cc_start: 0.6055 (tt0) cc_final: 0.5578 (mt-10) REVERT: D 213 GLU cc_start: 0.7400 (tt0) cc_final: 0.6840 (tp30) REVERT: D 242 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6846 (mt-10) outliers start: 26 outliers final: 16 residues processed: 144 average time/residue: 0.2311 time to fit residues: 50.1105 Evaluate side-chains 139 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 396 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 144 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.6382 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12952 Z= 0.208 Angle : 0.475 8.102 17628 Z= 0.238 Chirality : 0.040 0.282 1944 Planarity : 0.005 0.047 2204 Dihedral : 7.330 59.897 1888 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.68 % Allowed : 13.54 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.43 (0.22), residues: 1532 helix: 1.45 (0.17), residues: 984 sheet: None (None), residues: 0 loop : 0.18 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 94 HIS 0.003 0.001 HIS A 77 PHE 0.009 0.001 PHE C 359 TYR 0.021 0.001 TYR A 48 ARG 0.002 0.000 ARG C 320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.5751 (OUTLIER) cc_final: 0.5315 (mp) REVERT: A 107 MET cc_start: 0.7495 (mmp) cc_final: 0.5991 (mpp) REVERT: A 177 TRP cc_start: 0.5267 (t-100) cc_final: 0.4511 (m-90) REVERT: A 210 GLU cc_start: 0.5994 (tt0) cc_final: 0.5526 (mt-10) REVERT: A 213 GLU cc_start: 0.7375 (tt0) cc_final: 0.6793 (tp30) REVERT: A 242 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6910 (mt-10) REVERT: C 48 TYR cc_start: 0.7794 (t80) cc_final: 0.7392 (t80) REVERT: C 67 ILE cc_start: 0.5730 (OUTLIER) cc_final: 0.5272 (mp) REVERT: C 107 MET cc_start: 0.7639 (mmp) cc_final: 0.6041 (mpp) REVERT: C 117 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6135 (pp20) REVERT: C 177 TRP cc_start: 0.5308 (t-100) cc_final: 0.4580 (m-90) REVERT: C 210 GLU cc_start: 0.5955 (tt0) cc_final: 0.5480 (mt-10) REVERT: C 213 GLU cc_start: 0.7366 (tt0) cc_final: 0.6691 (mp0) REVERT: C 242 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6973 (mt-10) REVERT: B 67 ILE cc_start: 0.5744 (OUTLIER) cc_final: 0.5282 (mp) REVERT: B 107 MET cc_start: 0.7490 (mmp) cc_final: 0.5999 (mpp) REVERT: B 210 GLU cc_start: 0.6008 (tt0) cc_final: 0.5382 (mt-10) REVERT: B 242 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6786 (mt-10) REVERT: D 67 ILE cc_start: 0.5724 (OUTLIER) cc_final: 0.5264 (mp) REVERT: D 107 MET cc_start: 0.7516 (mmp) cc_final: 0.5984 (mpp) REVERT: D 177 TRP cc_start: 0.5340 (t-100) cc_final: 0.4743 (m-90) REVERT: D 210 GLU cc_start: 0.6047 (tt0) cc_final: 0.5518 (mt-10) REVERT: D 213 GLU cc_start: 0.7373 (tt0) cc_final: 0.6833 (tp30) REVERT: D 242 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6902 (mt-10) outliers start: 21 outliers final: 15 residues processed: 153 average time/residue: 0.2351 time to fit residues: 53.8148 Evaluate side-chains 148 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 389 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 70 optimal weight: 0.3980 chunk 102 optimal weight: 0.0170 chunk 155 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 98 optimal weight: 30.0000 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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: 0.6336 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12952 Z= 0.150 Angle : 0.446 8.015 17628 Z= 0.223 Chirality : 0.038 0.220 1944 Planarity : 0.005 0.043 2204 Dihedral : 6.711 59.436 1888 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.52 % Allowed : 13.94 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.75 (0.22), residues: 1532 helix: 1.67 (0.17), residues: 984 sheet: None (None), residues: 0 loop : 0.36 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 94 HIS 0.003 0.000 HIS C 383 PHE 0.013 0.001 PHE A 289 TYR 0.021 0.001 TYR A 48 ARG 0.002 0.000 ARG C 320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 1.349 Fit side-chains revert: symmetry clash REVERT: A 67 ILE cc_start: 0.5621 (OUTLIER) cc_final: 0.5185 (mp) REVERT: A 107 MET cc_start: 0.7494 (mmp) cc_final: 0.6080 (mpp) REVERT: A 177 TRP cc_start: 0.5294 (t-100) cc_final: 0.4617 (m-90) REVERT: A 210 GLU cc_start: 0.5944 (tt0) cc_final: 0.5456 (mt-10) REVERT: A 213 GLU cc_start: 0.7355 (tt0) cc_final: 0.6726 (mp0) REVERT: A 242 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6972 (mt-10) REVERT: A 430 MET cc_start: 0.7333 (mmt) cc_final: 0.7040 (mmt) REVERT: C 48 TYR cc_start: 0.7824 (t80) cc_final: 0.7371 (t80) REVERT: C 67 ILE cc_start: 0.5620 (OUTLIER) cc_final: 0.5188 (mp) REVERT: C 107 MET cc_start: 0.7542 (mmp) cc_final: 0.6000 (mpp) REVERT: C 117 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6226 (pp20) REVERT: C 177 TRP cc_start: 0.5348 (t-100) cc_final: 0.4682 (m-90) REVERT: C 210 GLU cc_start: 0.5896 (tt0) cc_final: 0.5404 (mt-10) REVERT: C 213 GLU cc_start: 0.7350 (tt0) cc_final: 0.6683 (mp0) REVERT: C 242 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6976 (mt-10) REVERT: B 67 ILE cc_start: 0.5618 (OUTLIER) cc_final: 0.5163 (mp) REVERT: B 107 MET cc_start: 0.7463 (mmp) cc_final: 0.6062 (mpp) REVERT: B 210 GLU cc_start: 0.5959 (tt0) cc_final: 0.5357 (mt-10) REVERT: B 242 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6804 (mt-10) REVERT: B 430 MET cc_start: 0.7311 (mmt) cc_final: 0.7021 (mmt) REVERT: B 458 LYS cc_start: 0.6769 (mttp) cc_final: 0.6324 (mttp) REVERT: D 67 ILE cc_start: 0.5596 (OUTLIER) cc_final: 0.5144 (mp) REVERT: D 107 MET cc_start: 0.7476 (mmp) cc_final: 0.6048 (mpp) REVERT: D 177 TRP cc_start: 0.5372 (t-100) cc_final: 0.4847 (m-90) REVERT: D 210 GLU cc_start: 0.6025 (tt0) cc_final: 0.5471 (mt-10) REVERT: D 213 GLU cc_start: 0.7350 (tt0) cc_final: 0.6971 (tp30) REVERT: D 242 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6893 (mt-10) REVERT: D 430 MET cc_start: 0.7352 (mmt) cc_final: 0.7047 (mmt) REVERT: D 458 LYS cc_start: 0.6720 (mttp) cc_final: 0.6373 (mttp) outliers start: 19 outliers final: 6 residues processed: 156 average time/residue: 0.2463 time to fit residues: 57.6971 Evaluate side-chains 148 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 377 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 114 optimal weight: 0.2980 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 51 optimal weight: 0.0870 chunk 127 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 108 optimal weight: 0.2980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.4422 r_free = 0.4422 target = 0.218393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.195422 restraints weight = 12994.774| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 1.07 r_work: 0.4066 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3988 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12952 Z= 0.151 Angle : 0.442 8.186 17628 Z= 0.220 Chirality : 0.038 0.198 1944 Planarity : 0.004 0.042 2204 Dihedral : 6.482 59.812 1888 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.96 % Allowed : 14.74 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.73 (0.22), residues: 1532 helix: 1.69 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : 0.19 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 94 HIS 0.002 0.000 HIS B 43 PHE 0.016 0.001 PHE B 289 TYR 0.022 0.001 TYR A 48 ARG 0.002 0.000 ARG A 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2487.40 seconds wall clock time: 46 minutes 24.00 seconds (2784.00 seconds total)