Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 6 09:28:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phl_13419/10_2023/7phl_13419_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phl_13419/10_2023/7phl_13419.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phl_13419/10_2023/7phl_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_13419/10_2023/7phl_13419_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phl_13419/10_2023/7phl_13419_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phl_13419/10_2023/7phl_13419.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phl_13419/10_2023/7phl_13419.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phl_13419/10_2023/7phl_13419_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phl_13419/10_2023/7phl_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-1.21rc1-5097/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: 6.84, per 1000 atoms: 0.54 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: 5.07 Conformation dependent library (CDL) restraints added in 1.8 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: 1.95 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: 5.38 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: 6853 17.73 - 35.46: 451 35.46 - 53.19: 128 53.19 - 70.91: 32 70.91 - 88.64: 16 Dihedral angle restraints: 7480 sinusoidal: 2912 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 7477 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.190 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 37.220 Find NCS groups from input model: 0.970 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.510 ------------------------------------------------------------------------------- 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 : 14.357 88.643 4520 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 *********************** 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 : 1.403 Fit side-chains outliers start: 12 outliers final: 0 residues processed: 204 average time/residue: 0.2807 time to fit residues: 80.3044 Evaluate side-chains 162 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.377 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 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: 1.2984 ------------------------------------------------------------------------------- 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: 0.6359 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12952 Z= 0.248 Angle : 0.528 8.733 17628 Z= 0.265 Chirality : 0.041 0.237 1944 Planarity : 0.005 0.050 2204 Dihedral : 8.724 58.549 1872 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.28 % Allowed : 8.09 % Favored : 90.62 % 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: 0.78 (0.21), residues: 1532 helix: 1.18 (0.17), residues: 956 sheet: None (None), residues: 0 loop : -0.53 (0.26), residues: 576 *********************** 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 177 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 172 average time/residue: 0.2287 time to fit residues: 58.8165 Evaluate side-chains 160 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 152 time to evaluate : 1.344 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1212 time to fit residues: 3.5814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 117 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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: 0.6447 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 12952 Z= 0.503 Angle : 0.630 9.503 17628 Z= 0.320 Chirality : 0.047 0.324 1944 Planarity : 0.005 0.062 2204 Dihedral : 8.579 59.349 1872 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.36 % Allowed : 11.94 % Favored : 86.70 % 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: 0.32 (0.21), residues: 1532 helix: 0.89 (0.16), residues: 976 sheet: None (None), residues: 0 loop : -0.93 (0.25), residues: 556 *********************** 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 154 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 154 average time/residue: 0.2269 time to fit residues: 53.0566 Evaluate side-chains 138 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 1.453 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1189 time to fit residues: 4.6838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 0.1980 chunk 40 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.6349 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12952 Z= 0.170 Angle : 0.468 8.540 17628 Z= 0.234 Chirality : 0.039 0.242 1944 Planarity : 0.004 0.047 2204 Dihedral : 7.499 59.387 1872 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.44 % Allowed : 11.54 % Favored : 87.02 % 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: 1.35 (0.22), residues: 1532 helix: 1.45 (0.17), residues: 976 sheet: None (None), residues: 0 loop : 0.01 (0.26), residues: 556 *********************** 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 161 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 154 average time/residue: 0.2219 time to fit residues: 51.8795 Evaluate side-chains 133 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 1.454 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1378 time to fit residues: 2.9014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 2 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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: 0.6455 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 12952 Z= 0.504 Angle : 0.611 9.149 17628 Z= 0.312 Chirality : 0.046 0.297 1944 Planarity : 0.005 0.058 2204 Dihedral : 8.134 59.970 1872 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.52 % Allowed : 12.82 % Favored : 85.66 % 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: 0.41 (0.21), residues: 1532 helix: 0.96 (0.17), residues: 980 sheet: None (None), residues: 0 loop : -0.89 (0.23), residues: 552 *********************** 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 137 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 1.497 Fit side-chains outliers start: 19 outliers final: 14 residues processed: 137 average time/residue: 0.2288 time to fit residues: 47.1662 Evaluate side-chains 128 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 1.257 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1099 time to fit residues: 4.6554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 12 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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: 0.6364 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12952 Z= 0.188 Angle : 0.465 8.662 17628 Z= 0.235 Chirality : 0.039 0.247 1944 Planarity : 0.004 0.046 2204 Dihedral : 7.031 58.187 1872 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.72 % Allowed : 13.54 % 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: 1.01 (0.21), residues: 1532 helix: 1.23 (0.17), residues: 1004 sheet: None (None), residues: 0 loop : -0.29 (0.26), residues: 528 *********************** 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 138 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 1.366 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 134 average time/residue: 0.2244 time to fit residues: 45.6476 Evaluate side-chains 125 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 1.437 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1403 time to fit residues: 2.7503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 85 optimal weight: 0.0070 chunk 110 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 91 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- 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: 0.6383 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12952 Z= 0.227 Angle : 0.480 9.712 17628 Z= 0.240 Chirality : 0.039 0.224 1944 Planarity : 0.005 0.048 2204 Dihedral : 6.705 58.693 1872 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.40 % Allowed : 14.34 % Favored : 85.26 % 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: 1.10 (0.21), residues: 1532 helix: 1.29 (0.17), residues: 1004 sheet: None (None), residues: 0 loop : -0.24 (0.26), residues: 528 *********************** 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 134 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.350 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 133 average time/residue: 0.2425 time to fit residues: 48.5548 Evaluate side-chains 128 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.411 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 45 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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: 0.6416 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12952 Z= 0.323 Angle : 0.522 9.168 17628 Z= 0.264 Chirality : 0.041 0.276 1944 Planarity : 0.005 0.051 2204 Dihedral : 7.009 59.129 1872 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.40 % Allowed : 14.82 % 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: 1.12 (0.22), residues: 1532 helix: 1.25 (0.17), residues: 984 sheet: None (None), residues: 0 loop : -0.06 (0.26), residues: 548 *********************** 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 122 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.359 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 122 average time/residue: 0.2518 time to fit residues: 45.5344 Evaluate side-chains 117 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1124 time to fit residues: 2.6573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.6408 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12952 Z= 0.305 Angle : 0.512 9.347 17628 Z= 0.258 Chirality : 0.040 0.153 1944 Planarity : 0.005 0.049 2204 Dihedral : 6.966 58.810 1872 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.32 % Allowed : 14.50 % Favored : 85.18 % 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: 1.01 (0.22), residues: 1532 helix: 1.15 (0.17), residues: 1004 sheet: None (None), residues: 0 loop : -0.12 (0.27), residues: 528 *********************** 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 117 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 1.365 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 117 average time/residue: 0.2537 time to fit residues: 44.0271 Evaluate side-chains 115 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 1.444 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1089 time to fit residues: 2.5779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 155 optimal weight: 0.0050 chunk 143 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 98 optimal weight: 20.0000 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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: 0.6347 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12952 Z= 0.164 Angle : 0.452 9.197 17628 Z= 0.226 Chirality : 0.037 0.126 1944 Planarity : 0.005 0.043 2204 Dihedral : 6.188 57.963 1872 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.08 % Allowed : 14.58 % Favored : 85.34 % 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: 1.51 (0.22), residues: 1532 helix: 1.48 (0.17), residues: 984 sheet: None (None), residues: 0 loop : 0.26 (0.27), residues: 548 ********************** 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 136 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 1.625 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.2372 time to fit residues: 48.2801 Evaluate side-chains 130 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.436 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 chunk 108 optimal weight: 5.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.4378 r_free = 0.4378 target = 0.213251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.195888 restraints weight = 12968.593| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 0.88 r_work: 0.4083 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.4007 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12952 Z= 0.294 Angle : 0.505 8.949 17628 Z= 0.256 Chirality : 0.040 0.167 1944 Planarity : 0.005 0.048 2204 Dihedral : 6.590 58.765 1872 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.16 % Allowed : 15.22 % 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: 1.27 (0.17), residues: 1004 sheet: None (None), residues: 0 loop : 0.06 (0.27), residues: 528 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2282.34 seconds wall clock time: 42 minutes 23.64 seconds (2543.64 seconds total)