Starting phenix.real_space_refine on Sat Mar 16 11:54:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sd3_40349/03_2024/8sd3_40349_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sd3_40349/03_2024/8sd3_40349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sd3_40349/03_2024/8sd3_40349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sd3_40349/03_2024/8sd3_40349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sd3_40349/03_2024/8sd3_40349_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sd3_40349/03_2024/8sd3_40349_updated.pdb" } resolution = 2.95 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= 0.000 sd= 0.006 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 P 8 5.49 5 S 36 5.16 5 C 5276 2.51 5 N 1156 2.21 5 O 1352 1.98 5 H 6824 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14656 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3544 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3544 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3544 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3544 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 122 Unusual residues: {' K': 3, 'POV': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 119 Unusual residues: {'POV': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 120 Unusual residues: {' K': 1, 'POV': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 119 Unusual residues: {'POV': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 6.80, per 1000 atoms: 0.46 Number of scatterers: 14656 At special positions: 0 Unit cell: (107.06, 107.06, 69.96, 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) K 4 19.00 S 36 16.00 P 8 15.00 O 1352 8.00 N 1156 7.00 C 5276 6.00 H 6824 1.00 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: 11.21 Conformation dependent library (CDL) restraints added in 1.6 seconds 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1808 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 0 sheets defined 80.2% alpha, 0.0% 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 172 through 176 removed outlier: 3.731A pdb=" N GLU A 176 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 206 removed outlier: 4.275A pdb=" N THR A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 245 removed outlier: 4.147A pdb=" N ALA A 234 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.846A pdb=" N ILE A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 289 through 309 removed outlier: 4.261A pdb=" N ILE A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG A 299 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ILE A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ARG A 302 " --> pdb=" O MET A 298 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEU A 306 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ALA A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ARG A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N HIS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 322 Processing helix chain 'A' and resid 324 through 349 Processing helix chain 'A' and resid 360 through 371 removed outlier: 4.146A pdb=" N TRP A 365 " --> pdb=" O PRO A 361 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 403 removed outlier: 3.759A pdb=" N ILE A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 427 Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.732A pdb=" N GLU B 176 " --> pdb=" O ASP B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 206 removed outlier: 4.275A pdb=" N THR B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 245 removed outlier: 4.147A pdb=" N ALA B 234 " --> pdb=" O VAL B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 255 No H-bonds generated for 'chain 'B' and resid 252 through 255' Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.846A pdb=" N ILE B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Proline residue: B 268 - end of helix Processing helix chain 'B' and resid 289 through 309 removed outlier: 4.261A pdb=" N ILE B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ILE B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU B 301 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ARG B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEU B 306 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ALA B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ARG B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N HIS B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 322 Processing helix chain 'B' and resid 324 through 349 Processing helix chain 'B' and resid 360 through 371 removed outlier: 4.147A pdb=" N TRP B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 403 removed outlier: 3.759A pdb=" N ILE B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 427 Processing helix chain 'C' and resid 172 through 176 removed outlier: 3.732A pdb=" N GLU C 176 " --> pdb=" O ASP C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 206 removed outlier: 4.275A pdb=" N THR C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 245 removed outlier: 4.147A pdb=" N ALA C 234 " --> pdb=" O VAL C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 255 No H-bonds generated for 'chain 'C' and resid 252 through 255' Processing helix chain 'C' and resid 257 through 276 removed outlier: 3.846A pdb=" N ILE C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Proline residue: C 268 - end of helix Processing helix chain 'C' and resid 289 through 309 removed outlier: 4.262A pdb=" N ILE C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG C 299 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ILE C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU C 301 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ARG C 302 " --> pdb=" O MET C 298 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU C 304 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU C 306 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ALA C 307 " --> pdb=" O ILE C 303 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ARG C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N HIS C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 322 Processing helix chain 'C' and resid 324 through 349 Processing helix chain 'C' and resid 360 through 371 removed outlier: 4.146A pdb=" N TRP C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 403 removed outlier: 3.760A pdb=" N ILE C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 427 Processing helix chain 'D' and resid 172 through 176 removed outlier: 3.731A pdb=" N GLU D 176 " --> pdb=" O ASP D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 206 removed outlier: 4.275A pdb=" N THR D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 245 removed outlier: 4.147A pdb=" N ALA D 234 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 255 No H-bonds generated for 'chain 'D' and resid 252 through 255' Processing helix chain 'D' and resid 257 through 276 removed outlier: 3.846A pdb=" N ILE D 266 " --> pdb=" O ASP D 262 " (cutoff:3.500A) Proline residue: D 268 - end of helix Processing helix chain 'D' and resid 289 through 309 removed outlier: 4.262A pdb=" N ILE D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ILE D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU D 301 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ARG D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE D 303 " --> pdb=" O ARG D 299 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU D 304 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEU D 306 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ALA D 307 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ARG D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N HIS D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 322 Processing helix chain 'D' and resid 324 through 349 Processing helix chain 'D' and resid 360 through 371 removed outlier: 4.146A pdb=" N TRP D 365 " --> pdb=" O PRO D 361 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 403 removed outlier: 3.759A pdb=" N ILE D 395 " --> pdb=" O GLY D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 427 504 hydrogen bonds defined for protein. 1284 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: 4.54 Time building geometry restraints manager: 11.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6812 1.03 - 1.22: 52 1.22 - 1.42: 3044 1.42 - 1.61: 4820 1.61 - 1.81: 68 Bond restraints: 14796 Sorted by residual: bond pdb=" C21 POV B1004 " pdb=" O21 POV B1004 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" C21 POV C1004 " pdb=" O21 POV C1004 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C21 POV D1004 " pdb=" O21 POV D1004 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C21 POV A1004 " pdb=" O21 POV A1004 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C21 POV A1003 " pdb=" O21 POV A1003 " ideal model delta sigma weight residual 1.330 1.456 -0.126 2.00e-02 2.50e+03 3.97e+01 ... (remaining 14791 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.86: 184 105.86 - 112.92: 17034 112.92 - 119.98: 4191 119.98 - 127.04: 4803 127.04 - 134.10: 88 Bond angle restraints: 26300 Sorted by residual: angle pdb=" C32 POV B1002 " pdb=" C31 POV B1002 " pdb=" O31 POV B1002 " ideal model delta sigma weight residual 110.66 121.01 -10.35 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C32 POV A1002 " pdb=" C31 POV A1002 " pdb=" O31 POV A1002 " ideal model delta sigma weight residual 110.66 120.96 -10.30 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C32 POV D1002 " pdb=" C31 POV D1002 " pdb=" O31 POV D1002 " ideal model delta sigma weight residual 110.66 120.96 -10.30 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C32 POV C1002 " pdb=" C31 POV C1002 " pdb=" O31 POV C1002 " ideal model delta sigma weight residual 110.66 120.95 -10.29 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C32 POV C1003 " pdb=" C31 POV C1003 " pdb=" O31 POV C1003 " ideal model delta sigma weight residual 110.66 120.68 -10.02 3.00e+00 1.11e-01 1.12e+01 ... (remaining 26295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.11: 6696 21.11 - 42.22: 320 42.22 - 63.32: 164 63.32 - 84.43: 24 84.43 - 105.54: 16 Dihedral angle restraints: 7220 sinusoidal: 3912 harmonic: 3308 Sorted by residual: dihedral pdb=" C3 POV D1001 " pdb=" C31 POV D1001 " pdb=" O31 POV D1001 " pdb=" C32 POV D1001 " ideal model delta sinusoidal sigma weight residual 172.61 -81.85 -105.54 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" C3 POV A1001 " pdb=" C31 POV A1001 " pdb=" O31 POV A1001 " pdb=" C32 POV A1001 " ideal model delta sinusoidal sigma weight residual 172.61 -81.87 -105.52 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" C3 POV C1001 " pdb=" C31 POV C1001 " pdb=" O31 POV C1001 " pdb=" C32 POV C1001 " ideal model delta sinusoidal sigma weight residual 172.61 -81.89 -105.50 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1110 0.067 - 0.134: 147 0.134 - 0.201: 3 0.201 - 0.268: 0 0.268 - 0.335: 4 Chirality restraints: 1264 Sorted by residual: chirality pdb=" CG LEU D 207 " pdb=" CB LEU D 207 " pdb=" CD1 LEU D 207 " pdb=" CD2 LEU D 207 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CG LEU A 207 " pdb=" CB LEU A 207 " pdb=" CD1 LEU A 207 " pdb=" CD2 LEU A 207 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CG LEU B 207 " pdb=" CB LEU B 207 " pdb=" CD1 LEU B 207 " pdb=" CD2 LEU B 207 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 1261 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 254 " -0.044 2.00e-02 2.50e+03 3.11e-02 2.90e+01 pdb=" CG PHE B 254 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE B 254 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE B 254 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE B 254 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE B 254 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 254 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE B 254 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE B 254 " 0.017 2.00e-02 2.50e+03 pdb=" HE1 PHE B 254 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 PHE B 254 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE B 254 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 254 " -0.044 2.00e-02 2.50e+03 3.11e-02 2.90e+01 pdb=" CG PHE A 254 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE A 254 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 254 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE A 254 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE A 254 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 254 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 254 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE A 254 " 0.017 2.00e-02 2.50e+03 pdb=" HE1 PHE A 254 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 PHE A 254 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 254 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 254 " 0.044 2.00e-02 2.50e+03 3.11e-02 2.90e+01 pdb=" CG PHE C 254 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE C 254 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 254 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE C 254 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE C 254 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 254 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE C 254 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE C 254 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 PHE C 254 " 0.012 2.00e-02 2.50e+03 pdb=" HE2 PHE C 254 " -0.004 2.00e-02 2.50e+03 pdb=" HZ PHE C 254 " 0.013 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.47: 8490 2.47 - 3.14: 39747 3.14 - 3.81: 49744 3.81 - 4.47: 74505 4.47 - 5.14: 112045 Nonbonded interactions: 284531 Sorted by model distance: nonbonded pdb=" HZ3 LYS D 356 " pdb=" O ASP D 378 " model vdw 1.808 1.850 nonbonded pdb=" HZ3 LYS A 356 " pdb=" O ASP A 378 " model vdw 1.808 1.850 nonbonded pdb=" HZ3 LYS B 356 " pdb=" O ASP B 378 " model vdw 1.808 1.850 nonbonded pdb=" HZ3 LYS C 356 " pdb=" O ASP C 378 " model vdw 1.808 1.850 nonbonded pdb=" O THR A 372 " pdb=" HG1 THR A 373 " model vdw 1.813 1.850 ... (remaining 284526 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 171 through 428 or (resid 1001 and (name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name O22)) or resid 1002 or (r \ esid 1003 and (name C1 or name C2 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28 or name C3 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name O21 or name O22 or name O31 or \ name O32)) or (resid 1004 and (name C1 or name C2 or name C21 or name C22 or nam \ e C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name O21 or \ name O22)) or resid 1005 through 1006)) selection = (chain 'B' and (resid 171 through 428 or resid 1000 through 1001 or (resid 1002 \ and (name C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name \ C25 or name C26 or name C27 or name C28 or name C3 or name C31 or name C32 or na \ me C33 or name C34 or name C35 or name O21 or name O22 or name O31 or name O32)) \ or (resid 1003 and (name C1 or name C2 or name C21 or name C22 or name C23 or n \ ame C24 or name C25 or name C26 or name C27 or name C28 or name O21 or name O22) \ ) or (resid 1004 through 1005 and (name C21 or name C22 or name C23 or name C24 \ or name C25 or name C26 or name O22)))) selection = (chain 'C' and (resid 171 through 428 or (resid 1001 and (name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name O22)) or resid 1002 or (r \ esid 1003 and (name C1 or name C2 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28 or name C3 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name O21 or name O22 or name O31 or \ name O32)) or (resid 1004 and (name C1 or name C2 or name C21 or name C22 or nam \ e C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name O21 or \ name O22)) or resid 1005 through 1006)) selection = (chain 'D' and (resid 171 through 428 or resid 1000 through 1001 or (resid 1002 \ and (name C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name \ C25 or name C26 or name C27 or name C28 or name C3 or name C31 or name C32 or na \ me C33 or name C34 or name C35 or name O21 or name O22 or name O31 or name O32)) \ or (resid 1003 and (name C1 or name C2 or name C21 or name C22 or name C23 or n \ ame C24 or name C25 or name C26 or name C27 or name C28 or name O21 or name O22) \ ) or (resid 1004 through 1005 and (name C21 or name C22 or name C23 or name C24 \ or name C25 or name C26 or name O22)))) } 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: 0.780 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: 0.210 Extract box with map and model: 3.840 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 49.040 Find NCS groups from input model: 0.820 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:10.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 : 0.010 0.128 7972 Z= 0.658 Angle : 1.079 10.351 10752 Z= 0.445 Chirality : 0.045 0.335 1264 Planarity : 0.005 0.047 1264 Dihedral : 16.417 105.541 2952 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: 1.86 (0.28), residues: 924 helix: 1.53 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 0.27 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 365 HIS 0.001 0.000 HIS B 227 PHE 0.085 0.003 PHE B 254 TYR 0.009 0.002 TYR A 376 ARG 0.004 0.001 ARG C 302 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.100 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 1.8424 time to fit residues: 222.2826 Evaluate side-chains 100 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 205 ASN B 179 ASN B 205 ASN C 179 ASN D 179 ASN D 205 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7972 Z= 0.176 Angle : 0.508 4.413 10752 Z= 0.261 Chirality : 0.036 0.121 1264 Planarity : 0.006 0.049 1264 Dihedral : 15.128 84.146 1328 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.55 % Allowed : 7.25 % Favored : 91.19 % 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: 2.00 (0.29), residues: 924 helix: 1.56 (0.20), residues: 740 sheet: None (None), residues: 0 loop : 0.67 (0.50), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 365 HIS 0.002 0.001 HIS C 227 PHE 0.015 0.001 PHE B 244 TYR 0.003 0.001 TYR B 270 ARG 0.002 0.000 ARG D 296 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.009 Fit side-chains outliers start: 12 outliers final: 2 residues processed: 126 average time/residue: 1.7637 time to fit residues: 239.9433 Evaluate side-chains 111 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain C residue 193 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 205 ASN B 179 ASN C 179 ASN D 179 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7972 Z= 0.226 Angle : 0.486 4.378 10752 Z= 0.255 Chirality : 0.036 0.121 1264 Planarity : 0.005 0.048 1264 Dihedral : 14.473 81.032 1328 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.91 % Allowed : 10.88 % Favored : 88.21 % 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: 1.89 (0.29), residues: 924 helix: 1.43 (0.20), residues: 740 sheet: None (None), residues: 0 loop : 0.90 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 365 HIS 0.002 0.000 HIS D 309 PHE 0.017 0.001 PHE D 244 TYR 0.004 0.001 TYR A 270 ARG 0.003 0.000 ARG D 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 1.196 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 128 average time/residue: 1.5881 time to fit residues: 221.3826 Evaluate side-chains 122 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 274 PHE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 193 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN B 179 ASN C 179 ASN D 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7972 Z= 0.313 Angle : 0.520 4.349 10752 Z= 0.277 Chirality : 0.038 0.131 1264 Planarity : 0.006 0.045 1264 Dihedral : 14.428 82.799 1328 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.91 % Allowed : 12.44 % Favored : 86.66 % 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: 1.57 (0.28), residues: 924 helix: 1.18 (0.20), residues: 740 sheet: None (None), residues: 0 loop : 0.88 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 365 HIS 0.002 0.001 HIS A 309 PHE 0.013 0.001 PHE C 244 TYR 0.005 0.001 TYR C 270 ARG 0.002 0.000 ARG D 296 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 1.197 Fit side-chains REVERT: A 324 TYR cc_start: 0.8296 (p90) cc_final: 0.7867 (p90) REVERT: B 324 TYR cc_start: 0.8287 (p90) cc_final: 0.7862 (p90) REVERT: C 324 TYR cc_start: 0.8292 (p90) cc_final: 0.7885 (p90) REVERT: D 349 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7885 (mt-10) outliers start: 7 outliers final: 7 residues processed: 133 average time/residue: 1.5142 time to fit residues: 219.6996 Evaluate side-chains 126 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 210 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN B 179 ASN C 179 ASN D 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7972 Z= 0.177 Angle : 0.458 4.306 10752 Z= 0.242 Chirality : 0.035 0.121 1264 Planarity : 0.005 0.045 1264 Dihedral : 13.585 81.580 1328 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.91 % Allowed : 12.31 % Favored : 86.79 % 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: 1.90 (0.29), residues: 924 helix: 1.38 (0.20), residues: 740 sheet: None (None), residues: 0 loop : 1.19 (0.50), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 365 HIS 0.001 0.000 HIS B 227 PHE 0.017 0.001 PHE A 244 TYR 0.004 0.001 TYR D 270 ARG 0.001 0.000 ARG B 299 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 1.270 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 129 average time/residue: 1.5750 time to fit residues: 221.1719 Evaluate side-chains 122 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain C residue 274 PHE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 193 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 85 optimal weight: 0.0770 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN B 179 ASN C 179 ASN D 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7972 Z= 0.195 Angle : 0.459 4.295 10752 Z= 0.244 Chirality : 0.035 0.125 1264 Planarity : 0.005 0.045 1264 Dihedral : 13.202 80.339 1328 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.65 % Allowed : 12.82 % Favored : 86.53 % 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: 2.01 (0.29), residues: 924 helix: 1.44 (0.20), residues: 740 sheet: None (None), residues: 0 loop : 1.28 (0.50), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 365 HIS 0.001 0.000 HIS D 227 PHE 0.018 0.001 PHE D 244 TYR 0.004 0.001 TYR C 270 ARG 0.003 0.000 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 130 time to evaluate : 0.886 Fit side-chains REVERT: B 324 TYR cc_start: 0.8280 (p90) cc_final: 0.7843 (p90) outliers start: 5 outliers final: 6 residues processed: 130 average time/residue: 1.5715 time to fit residues: 222.1913 Evaluate side-chains 131 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 125 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 274 PHE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 193 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN B 179 ASN C 179 ASN D 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7972 Z= 0.184 Angle : 0.451 4.304 10752 Z= 0.238 Chirality : 0.035 0.119 1264 Planarity : 0.005 0.045 1264 Dihedral : 12.917 78.547 1328 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.91 % Allowed : 12.69 % Favored : 86.40 % 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: 2.14 (0.29), residues: 924 helix: 1.52 (0.20), residues: 740 sheet: None (None), residues: 0 loop : 1.38 (0.50), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 365 HIS 0.001 0.000 HIS D 309 PHE 0.016 0.001 PHE D 244 TYR 0.004 0.001 TYR A 270 ARG 0.004 0.000 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 1.202 Fit side-chains REVERT: B 324 TYR cc_start: 0.8274 (p90) cc_final: 0.7880 (p90) outliers start: 7 outliers final: 7 residues processed: 134 average time/residue: 1.5388 time to fit residues: 224.7174 Evaluate side-chains 137 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 251 TRP Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 251 TRP Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 193 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN B 179 ASN C 179 ASN D 179 ASN D 419 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7972 Z= 0.174 Angle : 0.445 4.279 10752 Z= 0.236 Chirality : 0.035 0.119 1264 Planarity : 0.005 0.044 1264 Dihedral : 12.628 77.073 1328 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.17 % Allowed : 13.34 % Favored : 85.49 % 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: 2.23 (0.29), residues: 924 helix: 1.59 (0.20), residues: 740 sheet: None (None), residues: 0 loop : 1.39 (0.50), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 365 HIS 0.000 0.000 HIS C 227 PHE 0.015 0.001 PHE D 244 TYR 0.003 0.001 TYR A 270 ARG 0.004 0.000 ARG D 296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 1.165 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 135 average time/residue: 1.5644 time to fit residues: 231.8740 Evaluate side-chains 140 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 251 TRP Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 251 TRP Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 251 TRP Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 251 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN B 179 ASN C 179 ASN D 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7972 Z= 0.152 Angle : 0.440 5.341 10752 Z= 0.233 Chirality : 0.034 0.119 1264 Planarity : 0.005 0.044 1264 Dihedral : 12.293 75.885 1328 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.17 % Allowed : 13.73 % 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: 2.36 (0.30), residues: 924 helix: 1.68 (0.20), residues: 740 sheet: None (None), residues: 0 loop : 1.42 (0.50), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 365 HIS 0.001 0.000 HIS A 227 PHE 0.020 0.001 PHE A 244 TYR 0.003 0.001 TYR A 270 ARG 0.004 0.000 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 1.091 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 136 average time/residue: 1.5134 time to fit residues: 224.5241 Evaluate side-chains 138 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 251 TRP Chi-restraints excluded: chain B residue 251 TRP Chi-restraints excluded: chain C residue 251 TRP Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 251 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 419 GLN B 179 ASN C 179 ASN D 179 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7972 Z= 0.170 Angle : 0.452 5.352 10752 Z= 0.238 Chirality : 0.034 0.122 1264 Planarity : 0.005 0.044 1264 Dihedral : 12.209 74.735 1328 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.78 % Allowed : 15.03 % Favored : 84.20 % 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: 2.35 (0.30), residues: 924 helix: 1.68 (0.20), residues: 740 sheet: None (None), residues: 0 loop : 1.39 (0.50), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 365 HIS 0.001 0.000 HIS C 227 PHE 0.019 0.001 PHE C 244 TYR 0.003 0.001 TYR A 270 ARG 0.004 0.000 ARG A 296 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue LYS 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 407 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 1.109 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 132 average time/residue: 1.5692 time to fit residues: 225.3053 Evaluate side-chains 137 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 TRP Chi-restraints excluded: chain B residue 251 TRP Chi-restraints excluded: chain C residue 251 TRP Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 251 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 0.0770 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 419 GLN B 179 ASN C 179 ASN D 179 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.143101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.107805 restraints weight = 23866.351| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.99 r_work: 0.3042 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7972 Z= 0.145 Angle : 0.440 4.561 10752 Z= 0.232 Chirality : 0.034 0.119 1264 Planarity : 0.005 0.044 1264 Dihedral : 11.845 73.304 1328 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.65 % Allowed : 15.03 % Favored : 84.33 % 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: 2.32 (0.30), residues: 924 helix: 1.68 (0.20), residues: 748 sheet: None (None), residues: 0 loop : 1.26 (0.51), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 365 HIS 0.000 0.000 HIS C 309 PHE 0.019 0.001 PHE C 244 TYR 0.003 0.001 TYR A 270 ARG 0.004 0.000 ARG D 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5018.89 seconds wall clock time: 88 minutes 14.10 seconds (5294.10 seconds total)