Starting phenix.real_space_refine on Mon Mar 18 09:24:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sii_25142/03_2024/7sii_25142_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sii_25142/03_2024/7sii_25142.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sii_25142/03_2024/7sii_25142_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sii_25142/03_2024/7sii_25142_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sii_25142/03_2024/7sii_25142_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sii_25142/03_2024/7sii_25142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sii_25142/03_2024/7sii_25142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sii_25142/03_2024/7sii_25142_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sii_25142/03_2024/7sii_25142_trim_updated.pdb" } resolution = 3.45 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: 8 Type Number sf(0) Gaussians P 4 5.49 5 S 52 5.16 5 Cl 2 4.86 5 C 6580 2.51 5 N 1820 2.21 5 O 1834 1.98 5 F 8 1.80 5 H 10184 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20484 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5112 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 18, 'TRANS': 305} Chain breaks: 2 Chain: "B" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 5051 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 17, 'TRANS': 301} Chain breaks: 3 Chain: "C" Number of atoms: 5112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5112 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 18, 'TRANS': 305} Chain breaks: 2 Chain: "D" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 5051 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 17, 'TRANS': 301} Chain breaks: 3 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'9IM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'9IM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.52, per 1000 atoms: 0.46 Number of scatterers: 20484 At special positions: 0 Unit cell: (93.96, 98.28, 105.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 2 17.00 S 52 16.00 P 4 15.00 F 8 9.00 O 1834 8.00 N 1820 7.00 C 6580 6.00 H 10184 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: 16.04 Conformation dependent library (CDL) restraints added in 2.3 seconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 8 sheets defined 57.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 17 through 36 Processing helix chain 'A' and resid 40 through 76 removed outlier: 3.695A pdb=" N GLU A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N HIS A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N HIS A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N SER A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 92 through 108 Processing helix chain 'A' and resid 117 through 134 Processing helix chain 'A' and resid 141 through 151 Processing helix chain 'A' and resid 155 through 166 Processing helix chain 'A' and resid 168 through 185 Proline residue: A 173 - end of helix removed outlier: 4.247A pdb=" N GLN A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALA A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 263 through 273 Processing helix chain 'A' and resid 281 through 301 Processing helix chain 'A' and resid 325 through 334 Processing helix chain 'B' and resid 17 through 36 Processing helix chain 'B' and resid 40 through 69 Processing helix chain 'B' and resid 73 through 77 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 92 through 108 Processing helix chain 'B' and resid 118 through 134 Processing helix chain 'B' and resid 141 through 151 Processing helix chain 'B' and resid 156 through 166 Processing helix chain 'B' and resid 168 through 185 Proline residue: B 173 - end of helix removed outlier: 4.256A pdb=" N GLN B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ALA B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 215 No H-bonds generated for 'chain 'B' and resid 212 through 215' Processing helix chain 'B' and resid 263 through 273 Processing helix chain 'B' and resid 281 through 300 Processing helix chain 'B' and resid 325 through 334 Processing helix chain 'C' and resid 17 through 36 Processing helix chain 'C' and resid 40 through 76 removed outlier: 3.695A pdb=" N GLU C 68 " --> pdb=" O CYS C 64 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N HIS C 72 " --> pdb=" O GLU C 68 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N HIS C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N SER C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 92 through 108 Processing helix chain 'C' and resid 117 through 134 Processing helix chain 'C' and resid 141 through 151 Processing helix chain 'C' and resid 155 through 166 Processing helix chain 'C' and resid 168 through 185 Proline residue: C 173 - end of helix removed outlier: 4.247A pdb=" N GLN C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALA C 177 " --> pdb=" O PRO C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 215 No H-bonds generated for 'chain 'C' and resid 212 through 215' Processing helix chain 'C' and resid 263 through 273 Processing helix chain 'C' and resid 281 through 301 Processing helix chain 'C' and resid 325 through 334 Processing helix chain 'D' and resid 17 through 36 Processing helix chain 'D' and resid 40 through 69 Processing helix chain 'D' and resid 73 through 77 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 92 through 108 Processing helix chain 'D' and resid 118 through 134 Processing helix chain 'D' and resid 141 through 151 Processing helix chain 'D' and resid 156 through 166 Processing helix chain 'D' and resid 168 through 185 Proline residue: D 173 - end of helix removed outlier: 4.256A pdb=" N GLN D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA D 177 " --> pdb=" O PRO D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 215 No H-bonds generated for 'chain 'D' and resid 212 through 215' Processing helix chain 'D' and resid 263 through 273 Processing helix chain 'D' and resid 281 through 300 Processing helix chain 'D' and resid 325 through 334 Processing sheet with id= A, first strand: chain 'A' and resid 309 through 314 removed outlier: 5.836A pdb=" N LEU A 198 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE A 312 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE A 200 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N TYR A 314 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 202 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N TYR A 199 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL A 258 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU A 201 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLU A 260 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A 247 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR A 256 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR A 245 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLU A 246 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N PHE A 221 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU A 248 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 228 through 230 Processing sheet with id= C, first strand: chain 'B' and resid 309 through 314 removed outlier: 6.040A pdb=" N LEU B 198 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE B 312 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE B 200 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N TYR B 314 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU B 202 " --> pdb=" O TYR B 314 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N TYR B 199 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL B 258 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU B 201 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU B 260 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU B 247 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N THR B 256 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N TYR B 245 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL B 258 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N SER B 243 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLU B 246 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N PHE B 221 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LEU B 248 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 228 through 230 Processing sheet with id= E, first strand: chain 'C' and resid 309 through 314 removed outlier: 5.836A pdb=" N LEU C 198 " --> pdb=" O ARG C 310 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE C 312 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE C 200 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N TYR C 314 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU C 202 " --> pdb=" O TYR C 314 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N TYR C 199 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL C 258 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU C 201 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLU C 260 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU C 247 " --> pdb=" O ALA C 254 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR C 256 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR C 245 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLU C 246 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N PHE C 221 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU C 248 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 228 through 230 Processing sheet with id= G, first strand: chain 'D' and resid 309 through 314 removed outlier: 6.040A pdb=" N LEU D 198 " --> pdb=" O ARG D 310 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE D 312 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE D 200 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N TYR D 314 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU D 202 " --> pdb=" O TYR D 314 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N TYR D 199 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL D 258 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU D 201 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU D 260 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU D 247 " --> pdb=" O ALA D 254 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N THR D 256 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N TYR D 245 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL D 258 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N SER D 243 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLU D 246 " --> pdb=" O PHE D 221 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE D 221 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU D 248 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 228 through 230 546 hydrogen bonds defined for protein. 1596 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: 7.64 Time building geometry restraints manager: 16.79 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: 10144 1.03 - 1.23: 44 1.23 - 1.42: 4450 1.42 - 1.61: 6018 1.61 - 1.81: 74 Bond restraints: 20730 Sorted by residual: bond pdb=" C5 1SY D 401 " pdb=" N7 1SY D 401 " ideal model delta sigma weight residual 1.339 1.572 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C5 1SY B 401 " pdb=" N7 1SY B 401 " ideal model delta sigma weight residual 1.339 1.572 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C38 1SY B 401 " pdb=" O43 1SY B 401 " ideal model delta sigma weight residual 1.187 1.396 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C38 1SY D 401 " pdb=" O43 1SY D 401 " ideal model delta sigma weight residual 1.187 1.395 -0.208 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C37 1SY D 401 " pdb=" N35 1SY D 401 " ideal model delta sigma weight residual 1.328 1.530 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 20725 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.56: 1149 107.56 - 114.66: 24406 114.66 - 121.77: 8285 121.77 - 128.88: 3444 128.88 - 135.99: 96 Bond angle restraints: 37380 Sorted by residual: angle pdb=" O26 1SY D 401 " pdb=" P27 1SY D 401 " pdb=" O28 1SY D 401 " ideal model delta sigma weight residual 99.86 116.76 -16.90 3.00e+00 1.11e-01 3.17e+01 angle pdb=" O26 1SY B 401 " pdb=" P27 1SY B 401 " pdb=" O28 1SY B 401 " ideal model delta sigma weight residual 99.86 116.71 -16.85 3.00e+00 1.11e-01 3.16e+01 angle pdb=" C1' 1SY B 401 " pdb=" N9 1SY B 401 " pdb=" C4 1SY B 401 " ideal model delta sigma weight residual 133.88 118.32 15.56 3.00e+00 1.11e-01 2.69e+01 angle pdb=" C1' 1SY D 401 " pdb=" N9 1SY D 401 " pdb=" C4 1SY D 401 " ideal model delta sigma weight residual 133.88 118.35 15.53 3.00e+00 1.11e-01 2.68e+01 angle pdb=" C4 1SY B 401 " pdb=" N9 1SY B 401 " pdb=" C8 1SY B 401 " ideal model delta sigma weight residual 108.02 122.87 -14.85 3.00e+00 1.11e-01 2.45e+01 ... (remaining 37375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.56: 9415 33.56 - 67.12: 289 67.12 - 100.68: 6 100.68 - 134.24: 2 134.24 - 167.80: 4 Dihedral angle restraints: 9716 sinusoidal: 5376 harmonic: 4340 Sorted by residual: dihedral pdb=" C3' 1SY B 401 " pdb=" C16 1SY B 401 " pdb=" C4' 1SY B 401 " pdb=" O17 1SY B 401 " ideal model delta sinusoidal sigma weight residual 116.11 -76.09 -167.80 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C3' 1SY D 401 " pdb=" C16 1SY D 401 " pdb=" C4' 1SY D 401 " pdb=" O17 1SY D 401 " ideal model delta sinusoidal sigma weight residual 116.11 -76.38 -167.51 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C16 1SY D 401 " pdb=" O17 1SY D 401 " pdb=" P18 1SY D 401 " pdb=" O20 1SY D 401 " ideal model delta sinusoidal sigma weight residual 266.83 100.06 166.77 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 9713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1084 0.027 - 0.053: 353 0.053 - 0.080: 98 0.080 - 0.107: 35 0.107 - 0.133: 24 Chirality restraints: 1594 Sorted by residual: chirality pdb=" CA ILE D 10 " pdb=" N ILE D 10 " pdb=" C ILE D 10 " pdb=" CB ILE D 10 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE B 10 " pdb=" N ILE B 10 " pdb=" C ILE B 10 " pdb=" CB ILE B 10 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA ILE C 10 " pdb=" N ILE C 10 " pdb=" C ILE C 10 " pdb=" CB ILE C 10 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 1591 not shown) Planarity restraints: 3018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 72 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C HIS B 72 " -0.020 2.00e-02 2.50e+03 pdb=" O HIS B 72 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE B 73 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 72 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" C HIS D 72 " 0.020 2.00e-02 2.50e+03 pdb=" O HIS D 72 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE D 73 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 140 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO B 141 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 141 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 141 " -0.015 5.00e-02 4.00e+02 ... (remaining 3015 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 811 2.17 - 2.77: 39730 2.77 - 3.38: 58187 3.38 - 3.99: 72437 3.99 - 4.60: 116040 Nonbonded interactions: 287205 Sorted by model distance: nonbonded pdb=" OE1 GLU A 38 " pdb=" H GLU A 38 " model vdw 1.557 1.850 nonbonded pdb=" OE1 GLU C 38 " pdb=" H GLU C 38 " model vdw 1.558 1.850 nonbonded pdb=" O ILE C 73 " pdb=" H GLY C 79 " model vdw 1.640 1.850 nonbonded pdb=" O ILE A 73 " pdb=" H GLY A 79 " model vdw 1.640 1.850 nonbonded pdb=" O TYR A 245 " pdb=" HG1 THR A 256 " model vdw 1.656 1.850 ... (remaining 287200 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 3 through 110 or resid 116 through 335)) selection = (chain 'B' and resid 3 through 335) selection = (chain 'C' and (resid 3 through 110 or resid 116 through 335)) selection = (chain 'D' and resid 3 through 335) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.160 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: 0.310 Extract box with map and model: 2.120 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 68.000 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.008 0.233 10546 Z= 0.565 Angle : 0.739 16.900 14350 Z= 0.317 Chirality : 0.033 0.133 1594 Planarity : 0.003 0.026 1814 Dihedral : 13.748 167.796 3892 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.21 % Allowed : 4.97 % Favored : 92.82 % 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: 2.94 (0.25), residues: 1258 helix: 3.56 (0.18), residues: 730 sheet: -0.09 (0.43), residues: 144 loop : -0.56 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 161 HIS 0.003 0.001 HIS C 157 PHE 0.009 0.001 PHE B 291 TYR 0.010 0.001 TYR A 106 ARG 0.003 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 199 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 HIS cc_start: 0.7093 (t-90) cc_final: 0.6844 (m170) REVERT: A 236 LYS cc_start: 0.8114 (mmmm) cc_final: 0.7606 (mtpp) REVERT: B 66 LEU cc_start: 0.8651 (tt) cc_final: 0.8415 (tp) REVERT: B 86 ARG cc_start: 0.8248 (ttt90) cc_final: 0.7884 (ttm-80) REVERT: B 91 CYS cc_start: 0.7624 (t) cc_final: 0.7258 (t) REVERT: B 238 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.6095 (tmm-80) REVERT: C 41 GLU cc_start: 0.6950 (tm-30) cc_final: 0.6643 (tm-30) REVERT: C 106 TYR cc_start: 0.8495 (t80) cc_final: 0.8264 (t80) REVERT: C 185 HIS cc_start: 0.7084 (t-90) cc_final: 0.6683 (m170) REVERT: C 236 LYS cc_start: 0.8062 (mmmm) cc_final: 0.7733 (mtpp) REVERT: C 289 LYS cc_start: 0.8860 (mttp) cc_final: 0.8566 (mttm) REVERT: D 66 LEU cc_start: 0.8635 (tt) cc_final: 0.8391 (tp) REVERT: D 86 ARG cc_start: 0.8271 (ttt90) cc_final: 0.7877 (ttm-80) REVERT: D 91 CYS cc_start: 0.7592 (t) cc_final: 0.7224 (t) REVERT: D 238 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.6030 (tmm-80) REVERT: D 240 TYR cc_start: 0.8969 (m-80) cc_final: 0.7567 (m-80) outliers start: 24 outliers final: 8 residues processed: 211 average time/residue: 0.4700 time to fit residues: 139.9096 Evaluate side-chains 161 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 266 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10546 Z= 0.184 Angle : 0.475 4.084 14350 Z= 0.234 Chirality : 0.034 0.137 1594 Planarity : 0.004 0.039 1814 Dihedral : 11.487 177.445 1526 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.38 % Allowed : 7.92 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.25), residues: 1258 helix: 3.51 (0.18), residues: 740 sheet: -0.06 (0.44), residues: 144 loop : -0.65 (0.35), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 161 HIS 0.003 0.001 HIS B 157 PHE 0.008 0.001 PHE B 279 TYR 0.010 0.001 TYR C 106 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 170 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8225 (mmmm) cc_final: 0.7982 (mtpp) REVERT: A 240 TYR cc_start: 0.7967 (m-80) cc_final: 0.7742 (m-80) REVERT: B 86 ARG cc_start: 0.8265 (ttt90) cc_final: 0.7966 (ttm-80) REVERT: B 91 CYS cc_start: 0.7640 (t) cc_final: 0.7290 (t) REVERT: C 185 HIS cc_start: 0.7150 (t-90) cc_final: 0.6819 (m170) REVERT: C 236 LYS cc_start: 0.8251 (mmmm) cc_final: 0.8004 (mtpp) REVERT: C 240 TYR cc_start: 0.7979 (m-80) cc_final: 0.7754 (m-80) REVERT: D 86 ARG cc_start: 0.8264 (ttt90) cc_final: 0.7958 (ttm-80) REVERT: D 91 CYS cc_start: 0.7617 (t) cc_final: 0.7241 (t) outliers start: 15 outliers final: 9 residues processed: 176 average time/residue: 0.4537 time to fit residues: 114.9826 Evaluate side-chains 162 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 263 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10546 Z= 0.322 Angle : 0.543 4.849 14350 Z= 0.274 Chirality : 0.037 0.187 1594 Planarity : 0.004 0.027 1814 Dihedral : 10.856 167.592 1512 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.93 % Allowed : 9.76 % Favored : 88.31 % 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: 2.54 (0.25), residues: 1258 helix: 3.17 (0.19), residues: 748 sheet: -0.15 (0.42), residues: 154 loop : -0.82 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 161 HIS 0.006 0.001 HIS D 157 PHE 0.014 0.001 PHE B 105 TYR 0.025 0.001 TYR C 106 ARG 0.003 0.000 ARG C 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8348 (mmmm) cc_final: 0.7977 (mtpp) REVERT: B 86 ARG cc_start: 0.8381 (ttt90) cc_final: 0.8044 (ttm-80) REVERT: B 308 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7804 (p0) REVERT: C 236 LYS cc_start: 0.8352 (mmmm) cc_final: 0.7979 (mtpp) REVERT: D 86 ARG cc_start: 0.8344 (ttt90) cc_final: 0.8025 (ttm-80) REVERT: D 308 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.7847 (p0) outliers start: 21 outliers final: 15 residues processed: 160 average time/residue: 0.4358 time to fit residues: 100.4191 Evaluate side-chains 153 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 308 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10546 Z= 0.256 Angle : 0.499 4.188 14350 Z= 0.249 Chirality : 0.035 0.138 1594 Planarity : 0.004 0.027 1814 Dihedral : 10.634 163.661 1510 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.66 % Allowed : 10.50 % Favored : 87.85 % 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: 2.63 (0.25), residues: 1258 helix: 3.28 (0.19), residues: 740 sheet: -0.20 (0.43), residues: 144 loop : -0.75 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 161 HIS 0.003 0.001 HIS D 157 PHE 0.010 0.001 PHE B 105 TYR 0.015 0.001 TYR C 106 ARG 0.002 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 TYR cc_start: 0.7969 (m-80) cc_final: 0.7675 (m-80) REVERT: B 86 ARG cc_start: 0.8343 (ttt90) cc_final: 0.8017 (ttm-80) REVERT: C 240 TYR cc_start: 0.7977 (m-80) cc_final: 0.7680 (m-80) REVERT: D 86 ARG cc_start: 0.8336 (ttt90) cc_final: 0.8011 (ttm-80) outliers start: 18 outliers final: 18 residues processed: 159 average time/residue: 0.4705 time to fit residues: 105.5882 Evaluate side-chains 157 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 296 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10546 Z= 0.228 Angle : 0.487 4.059 14350 Z= 0.242 Chirality : 0.034 0.152 1594 Planarity : 0.004 0.028 1814 Dihedral : 10.438 158.766 1510 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.12 % Allowed : 10.68 % Favored : 87.20 % 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: 2.65 (0.25), residues: 1258 helix: 3.28 (0.19), residues: 742 sheet: -0.23 (0.43), residues: 144 loop : -0.70 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 34 HIS 0.003 0.001 HIS D 157 PHE 0.010 0.001 PHE B 105 TYR 0.016 0.001 TYR C 106 ARG 0.002 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8390 (mtpt) cc_final: 0.8053 (mtpp) REVERT: A 240 TYR cc_start: 0.7952 (m-80) cc_final: 0.7651 (m-80) REVERT: B 86 ARG cc_start: 0.8333 (ttt90) cc_final: 0.8014 (ttm-80) REVERT: C 240 TYR cc_start: 0.7967 (m-80) cc_final: 0.7679 (m-80) REVERT: D 86 ARG cc_start: 0.8333 (ttt90) cc_final: 0.8004 (ttm-80) outliers start: 23 outliers final: 16 residues processed: 161 average time/residue: 0.4807 time to fit residues: 109.4542 Evaluate side-chains 156 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 140 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 296 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 10546 Z= 0.444 Angle : 0.594 5.281 14350 Z= 0.303 Chirality : 0.038 0.139 1594 Planarity : 0.004 0.029 1814 Dihedral : 10.651 158.056 1510 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.39 % Allowed : 11.42 % Favored : 86.19 % 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: 2.09 (0.25), residues: 1258 helix: 2.81 (0.19), residues: 740 sheet: -0.34 (0.41), residues: 154 loop : -0.93 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 161 HIS 0.004 0.001 HIS C 332 PHE 0.012 0.002 PHE B 105 TYR 0.027 0.002 TYR A 106 ARG 0.002 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.7987 (t80) cc_final: 0.7755 (t80) REVERT: A 289 LYS cc_start: 0.9279 (mttp) cc_final: 0.8914 (mttp) REVERT: B 86 ARG cc_start: 0.8445 (ttt90) cc_final: 0.8121 (ttm-80) REVERT: B 150 LYS cc_start: 0.8984 (ttpt) cc_final: 0.8718 (ttpp) REVERT: B 218 ASN cc_start: 0.7903 (t0) cc_final: 0.7380 (t0) REVERT: B 308 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.7672 (p0) REVERT: C 107 TYR cc_start: 0.7949 (t80) cc_final: 0.7712 (t80) REVERT: D 86 ARG cc_start: 0.8446 (ttt90) cc_final: 0.8105 (ttm-80) REVERT: D 218 ASN cc_start: 0.7907 (t0) cc_final: 0.7377 (t0) REVERT: D 308 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7740 (p0) outliers start: 26 outliers final: 22 residues processed: 157 average time/residue: 0.5097 time to fit residues: 111.6315 Evaluate side-chains 154 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain C residue 186 TYR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 308 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10546 Z= 0.140 Angle : 0.467 3.959 14350 Z= 0.231 Chirality : 0.034 0.137 1594 Planarity : 0.004 0.031 1814 Dihedral : 10.087 151.781 1510 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.84 % Allowed : 12.34 % Favored : 85.82 % 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: 2.66 (0.25), residues: 1258 helix: 3.31 (0.19), residues: 738 sheet: -0.37 (0.42), residues: 144 loop : -0.65 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 34 HIS 0.002 0.000 HIS A 7 PHE 0.008 0.001 PHE B 105 TYR 0.019 0.001 TYR A 106 ARG 0.002 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.7941 (t80) cc_final: 0.7731 (t80) REVERT: A 236 LYS cc_start: 0.8384 (mtpt) cc_final: 0.8043 (mtpp) REVERT: A 240 TYR cc_start: 0.7911 (m-80) cc_final: 0.7614 (m-80) REVERT: B 86 ARG cc_start: 0.8305 (ttt90) cc_final: 0.7985 (ttm-80) REVERT: B 104 TYR cc_start: 0.8032 (t80) cc_final: 0.7789 (t80) REVERT: C 107 TYR cc_start: 0.7886 (t80) cc_final: 0.7673 (t80) REVERT: C 240 TYR cc_start: 0.7921 (m-80) cc_final: 0.7632 (m-80) REVERT: D 86 ARG cc_start: 0.8302 (ttt90) cc_final: 0.7973 (ttm-80) outliers start: 20 outliers final: 17 residues processed: 160 average time/residue: 0.4804 time to fit residues: 108.8397 Evaluate side-chains 160 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 296 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10546 Z= 0.161 Angle : 0.467 3.922 14350 Z= 0.229 Chirality : 0.033 0.132 1594 Planarity : 0.004 0.030 1814 Dihedral : 9.372 136.132 1510 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.38 % Allowed : 12.89 % Favored : 85.73 % 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: 2.76 (0.25), residues: 1258 helix: 3.38 (0.19), residues: 740 sheet: -0.33 (0.42), residues: 144 loop : -0.60 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 34 HIS 0.003 0.000 HIS D 157 PHE 0.010 0.001 PHE B 105 TYR 0.009 0.001 TYR A 46 ARG 0.001 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 153 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7057 (tm-30) cc_final: 0.6787 (tm-30) REVERT: A 107 TYR cc_start: 0.7967 (t80) cc_final: 0.7744 (t80) REVERT: A 236 LYS cc_start: 0.8361 (mtpt) cc_final: 0.8035 (mtpp) REVERT: A 240 TYR cc_start: 0.7910 (m-80) cc_final: 0.7629 (m-80) REVERT: B 86 ARG cc_start: 0.8289 (ttt90) cc_final: 0.7964 (ttm-80) REVERT: C 107 TYR cc_start: 0.7932 (t80) cc_final: 0.7710 (t80) REVERT: C 236 LYS cc_start: 0.8391 (mtpt) cc_final: 0.8043 (mtpp) REVERT: C 240 TYR cc_start: 0.7929 (m-80) cc_final: 0.7655 (m-80) REVERT: D 86 ARG cc_start: 0.8284 (ttt90) cc_final: 0.7951 (ttm-80) REVERT: D 106 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.7055 (t80) outliers start: 15 outliers final: 14 residues processed: 163 average time/residue: 0.4553 time to fit residues: 106.7389 Evaluate side-chains 164 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 296 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10546 Z= 0.182 Angle : 0.474 5.123 14350 Z= 0.232 Chirality : 0.034 0.137 1594 Planarity : 0.004 0.030 1814 Dihedral : 8.676 113.775 1510 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.75 % Allowed : 12.43 % Favored : 85.82 % 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: 2.80 (0.25), residues: 1258 helix: 3.40 (0.19), residues: 740 sheet: -0.36 (0.43), residues: 144 loop : -0.53 (0.35), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 34 HIS 0.003 0.000 HIS D 157 PHE 0.010 0.001 PHE B 105 TYR 0.023 0.001 TYR A 106 ARG 0.001 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 155 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6876 (tm-30) REVERT: A 107 TYR cc_start: 0.7966 (t80) cc_final: 0.7753 (t80) REVERT: A 236 LYS cc_start: 0.8335 (mtpt) cc_final: 0.8010 (mtpp) REVERT: A 240 TYR cc_start: 0.7960 (m-80) cc_final: 0.7693 (m-80) REVERT: B 86 ARG cc_start: 0.8295 (ttt90) cc_final: 0.7967 (ttm-80) REVERT: B 104 TYR cc_start: 0.7879 (t80) cc_final: 0.7660 (t80) REVERT: C 107 TYR cc_start: 0.7953 (t80) cc_final: 0.7736 (t80) REVERT: C 236 LYS cc_start: 0.8368 (mtpt) cc_final: 0.8044 (mtpp) REVERT: C 240 TYR cc_start: 0.7928 (m-80) cc_final: 0.7657 (m-80) REVERT: D 86 ARG cc_start: 0.8286 (ttt90) cc_final: 0.7950 (ttm-80) REVERT: D 106 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.7076 (t80) outliers start: 19 outliers final: 17 residues processed: 168 average time/residue: 0.4716 time to fit residues: 112.0724 Evaluate side-chains 169 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 296 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 99 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 61 optimal weight: 0.0670 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10546 Z= 0.177 Angle : 0.472 4.887 14350 Z= 0.231 Chirality : 0.034 0.138 1594 Planarity : 0.004 0.032 1814 Dihedral : 7.719 112.859 1510 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.57 % Allowed : 12.62 % Favored : 85.82 % 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: 2.80 (0.25), residues: 1258 helix: 3.37 (0.19), residues: 742 sheet: -0.34 (0.43), residues: 144 loop : -0.48 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 34 HIS 0.003 0.000 HIS D 157 PHE 0.008 0.001 PHE B 105 TYR 0.008 0.001 TYR C 46 ARG 0.001 0.000 ARG C 178 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 151 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6919 (tm-30) REVERT: A 107 TYR cc_start: 0.7949 (t80) cc_final: 0.7739 (t80) REVERT: A 236 LYS cc_start: 0.8354 (mtpt) cc_final: 0.8035 (mtpp) REVERT: A 240 TYR cc_start: 0.7946 (m-80) cc_final: 0.7686 (m-80) REVERT: B 86 ARG cc_start: 0.8284 (ttt90) cc_final: 0.7955 (ttm-80) REVERT: B 150 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8633 (ttpp) REVERT: C 107 TYR cc_start: 0.7952 (t80) cc_final: 0.7739 (t80) REVERT: C 224 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7731 (ttmt) REVERT: C 236 LYS cc_start: 0.8350 (mtpt) cc_final: 0.8024 (mtpp) REVERT: C 240 TYR cc_start: 0.7926 (m-80) cc_final: 0.7666 (m-80) REVERT: D 86 ARG cc_start: 0.8280 (ttt90) cc_final: 0.7942 (ttm-80) REVERT: D 106 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.7024 (t80) outliers start: 17 outliers final: 16 residues processed: 163 average time/residue: 0.4637 time to fit residues: 107.1965 Evaluate side-chains 168 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 151 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 296 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 41 optimal weight: 0.0570 chunk 102 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.121550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.102068 restraints weight = 45206.880| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.43 r_work: 0.3035 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10546 Z= 0.264 Angle : 0.509 5.202 14350 Z= 0.252 Chirality : 0.035 0.137 1594 Planarity : 0.004 0.031 1814 Dihedral : 7.633 114.053 1510 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.75 % Allowed : 12.52 % Favored : 85.73 % 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: 2.65 (0.25), residues: 1258 helix: 3.24 (0.19), residues: 744 sheet: -0.35 (0.43), residues: 144 loop : -0.56 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 34 HIS 0.004 0.001 HIS D 157 PHE 0.010 0.001 PHE B 105 TYR 0.025 0.001 TYR A 106 ARG 0.002 0.000 ARG C 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4248.60 seconds wall clock time: 76 minutes 54.20 seconds (4614.20 seconds total)