Starting phenix.real_space_refine on Mon Mar 11 09:40:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wha_21669/03_2024/6wha_21669_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wha_21669/03_2024/6wha_21669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wha_21669/03_2024/6wha_21669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wha_21669/03_2024/6wha_21669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wha_21669/03_2024/6wha_21669_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wha_21669/03_2024/6wha_21669_updated.pdb" } resolution = 3.36 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= 0.005 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 5016 2.51 5 N 1355 2.21 5 O 1473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 185": "NH1" <-> "NH2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E GLU 222": "OE1" <-> "OE2" 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: 7888 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1679 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 8, 'TRANS': 235} Chain breaks: 5 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 129 Chain: "B" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1650 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 206} Chain breaks: 4 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2471 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 99 Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1712 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'U0G': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.83, per 1000 atoms: 0.61 Number of scatterers: 7888 At special positions: 0 Unit cell: (97.1394, 113.329, 121.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1473 8.00 N 1355 7.00 C 5016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 2.88 Conformation dependent library (CDL) restraints added in 1.6 seconds 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 14 sheets defined 32.6% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 85 through 98 Processing helix chain 'A' and resid 110 through 136 removed outlier: 3.599A pdb=" N MET A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 146 through 178 removed outlier: 4.377A pdb=" N VAL A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 191 through 216 Proline residue: A 209 - end of helix removed outlier: 4.366A pdb=" N VAL A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 221 No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 232 through 243 Processing helix chain 'A' and resid 246 through 261 Processing helix chain 'A' and resid 317 through 346 removed outlier: 3.802A pdb=" N LYS A 323 " --> pdb=" O GLN A 319 " (cutoff:3.500A) Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 355 through 381 Proline residue: A 377 - end of helix removed outlier: 3.726A pdb=" N TYR A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 392 Processing helix chain 'B' and resid 7 through 32 removed outlier: 3.589A pdb=" N GLU B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 146 through 155 Processing helix chain 'B' and resid 160 through 163 No H-bonds generated for 'chain 'B' and resid 160 through 163' Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 184 through 202 removed outlier: 3.813A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 242 Processing helix chain 'C' and resid 4 through 22 Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing sheet with id= A, first strand: chain 'B' and resid 36 through 39 removed outlier: 7.053A pdb=" N ALA B 105 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU B 39 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE B 107 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER B 138 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N PHE B 108 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE B 140 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL B 110 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE B 142 " --> pdb=" O VAL B 110 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 69 through 75 removed outlier: 3.713A pdb=" N ASP B 85 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 72 " --> pdb=" O MET B 83 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B 83 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.842A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 111 through 115 removed outlier: 3.705A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.984A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.809A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 229 through 232 removed outlier: 6.862A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.633A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 318 through 320 removed outlier: 3.555A pdb=" N LYS C 337 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.627A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.740A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 143 through 148 Processing sheet with id= N, first strand: chain 'E' and resid 214 through 219 removed outlier: 3.647A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 1011 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1289 1.26 - 1.41: 2048 1.41 - 1.55: 4643 1.55 - 1.70: 1 1.70 - 1.84: 61 Bond restraints: 8042 Sorted by residual: bond pdb=" C05 U0G A 501 " pdb=" C06 U0G A 501 " ideal model delta sigma weight residual 1.422 1.536 -0.114 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C22 U0G A 501 " pdb=" O23 U0G A 501 " ideal model delta sigma weight residual 1.354 1.464 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" N ILE C 93 " pdb=" CA ILE C 93 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.00e-03 1.23e+04 1.68e+01 bond pdb=" N VAL E 135 " pdb=" CA VAL E 135 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.00e-03 1.23e+04 1.68e+01 bond pdb=" N VAL D 54 " pdb=" CA VAL D 54 " ideal model delta sigma weight residual 1.462 1.495 -0.033 8.70e-03 1.32e+04 1.46e+01 ... (remaining 8037 not shown) Histogram of bond angle deviations from ideal: 98.52 - 114.81: 4909 114.81 - 131.09: 6010 131.09 - 147.37: 33 147.37 - 163.65: 0 163.65 - 179.94: 1 Bond angle restraints: 10953 Sorted by residual: angle pdb=" CA GLY E 10 " pdb=" C GLY E 10 " pdb=" O GLY E 10 " ideal model delta sigma weight residual 122.37 117.88 4.49 7.30e-01 1.88e+00 3.78e+01 angle pdb=" N PRO A 209 " pdb=" CA PRO A 209 " pdb=" C PRO A 209 " ideal model delta sigma weight residual 113.53 120.38 -6.85 1.39e+00 5.18e-01 2.43e+01 angle pdb=" CA GLY E 230 " pdb=" C GLY E 230 " pdb=" O GLY E 230 " ideal model delta sigma weight residual 121.88 118.38 3.50 7.80e-01 1.64e+00 2.02e+01 angle pdb=" N CYS A 337 " pdb=" CA CYS A 337 " pdb=" C CYS A 337 " ideal model delta sigma weight residual 109.81 119.50 -9.69 2.21e+00 2.05e-01 1.92e+01 angle pdb=" CA VAL B 86 " pdb=" C VAL B 86 " pdb=" O VAL B 86 " ideal model delta sigma weight residual 121.68 118.42 3.26 7.90e-01 1.60e+00 1.70e+01 ... (remaining 10948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.04: 4381 21.04 - 42.09: 272 42.09 - 63.13: 38 63.13 - 84.18: 5 84.18 - 105.22: 3 Dihedral angle restraints: 4699 sinusoidal: 1595 harmonic: 3104 Sorted by residual: dihedral pdb=" C THR E 198 " pdb=" N THR E 198 " pdb=" CA THR E 198 " pdb=" CB THR E 198 " ideal model delta harmonic sigma weight residual -122.00 -132.23 10.23 0 2.50e+00 1.60e-01 1.67e+01 dihedral pdb=" C ARG E 179 " pdb=" N ARG E 179 " pdb=" CA ARG E 179 " pdb=" CB ARG E 179 " ideal model delta harmonic sigma weight residual -122.60 -132.45 9.85 0 2.50e+00 1.60e-01 1.55e+01 dihedral pdb=" C TYR E 102 " pdb=" N TYR E 102 " pdb=" CA TYR E 102 " pdb=" CB TYR E 102 " ideal model delta harmonic sigma weight residual -122.60 -131.81 9.21 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 4696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 748 0.063 - 0.126: 357 0.126 - 0.189: 144 0.189 - 0.251: 32 0.251 - 0.314: 4 Chirality restraints: 1285 Sorted by residual: chirality pdb=" CA THR E 198 " pdb=" N THR E 198 " pdb=" C THR E 198 " pdb=" CB THR E 198 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA ARG E 179 " pdb=" N ARG E 179 " pdb=" C ARG E 179 " pdb=" CB ARG E 179 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA LEU C 79 " pdb=" N LEU C 79 " pdb=" C LEU C 79 " pdb=" CB LEU C 79 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 1282 not shown) Planarity restraints: 1392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 240 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C PHE A 240 " 0.057 2.00e-02 2.50e+03 pdb=" O PHE A 240 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL A 241 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 163 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.53e+00 pdb=" C ILE A 163 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE A 163 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 164 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 179 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ARG E 179 " 0.039 2.00e-02 2.50e+03 pdb=" O ARG E 179 " -0.015 2.00e-02 2.50e+03 pdb=" N MET E 180 " -0.013 2.00e-02 2.50e+03 ... (remaining 1389 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1875 2.81 - 3.33: 6958 3.33 - 3.85: 11351 3.85 - 4.38: 13094 4.38 - 4.90: 23538 Nonbonded interactions: 56816 Sorted by model distance: nonbonded pdb=" O SER E 85 " pdb=" OG SER E 85 " model vdw 2.284 2.440 nonbonded pdb=" O SER B 204 " pdb=" OG SER B 204 " model vdw 2.291 2.440 nonbonded pdb=" O ASP C 195 " pdb=" OG1 THR C 196 " model vdw 2.381 2.440 nonbonded pdb=" O ASP C 163 " pdb=" OG1 THR C 164 " model vdw 2.384 2.440 nonbonded pdb=" OG SER C 161 " pdb=" N GLY C 162 " model vdw 2.391 2.520 ... (remaining 56811 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.240 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.200 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.012 0.114 8042 Z= 0.795 Angle : 1.196 9.929 10953 Z= 0.828 Chirality : 0.084 0.314 1285 Planarity : 0.005 0.049 1392 Dihedral : 13.683 105.222 2683 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.99 % Allowed : 15.99 % Favored : 81.01 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.26), residues: 1042 helix: 1.17 (0.28), residues: 352 sheet: 0.33 (0.35), residues: 263 loop : -1.54 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 169 HIS 0.009 0.002 HIS C 54 PHE 0.031 0.002 PHE B 197 TYR 0.023 0.002 TYR C 289 ARG 0.007 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 0.978 Fit side-chains REVERT: A 343 ASN cc_start: 0.6964 (t0) cc_final: 0.6685 (t0) REVERT: B 73 LYS cc_start: 0.8452 (ttpt) cc_final: 0.8073 (tmtt) REVERT: B 126 LYS cc_start: 0.8836 (tttt) cc_final: 0.8467 (ttpt) REVERT: B 164 PHE cc_start: 0.7415 (m-80) cc_final: 0.7177 (m-80) REVERT: B 166 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6257 (tm-30) REVERT: B 195 LYS cc_start: 0.8872 (tmmt) cc_final: 0.8599 (tppt) REVERT: C 76 ASP cc_start: 0.7410 (p0) cc_final: 0.7003 (p0) REVERT: C 153 ASP cc_start: 0.7201 (m-30) cc_final: 0.6999 (m-30) REVERT: C 268 ASN cc_start: 0.6963 (m-40) cc_final: 0.6618 (t0) REVERT: D 42 GLU cc_start: 0.7674 (tt0) cc_final: 0.7413 (tt0) REVERT: E 116 THR cc_start: 0.8275 (t) cc_final: 0.8058 (m) outliers start: 23 outliers final: 14 residues processed: 146 average time/residue: 0.2166 time to fit residues: 41.8689 Evaluate side-chains 115 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 0.2980 chunk 96 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN C 125 ASN C 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8042 Z= 0.159 Angle : 0.531 8.091 10953 Z= 0.285 Chirality : 0.043 0.136 1285 Planarity : 0.003 0.038 1392 Dihedral : 6.630 103.555 1166 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.99 % Allowed : 17.17 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1042 helix: 2.28 (0.27), residues: 353 sheet: 0.34 (0.33), residues: 269 loop : -1.38 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 339 HIS 0.003 0.001 HIS C 54 PHE 0.014 0.001 PHE C 199 TYR 0.012 0.001 TYR A 174 ARG 0.005 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 0.894 Fit side-chains REVERT: A 343 ASN cc_start: 0.6713 (t0) cc_final: 0.6434 (t0) REVERT: B 17 LYS cc_start: 0.8228 (mtmt) cc_final: 0.7521 (mttt) REVERT: B 73 LYS cc_start: 0.8402 (ttpt) cc_final: 0.8098 (tmtt) REVERT: B 126 LYS cc_start: 0.8712 (tttt) cc_final: 0.8432 (ttpt) REVERT: B 164 PHE cc_start: 0.7441 (m-80) cc_final: 0.7155 (m-80) REVERT: B 166 GLU cc_start: 0.6869 (tm-30) cc_final: 0.6312 (tm-30) REVERT: B 195 LYS cc_start: 0.8685 (tmmt) cc_final: 0.8405 (tppt) REVERT: B 242 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7305 (tt0) REVERT: C 268 ASN cc_start: 0.6859 (m-40) cc_final: 0.6151 (t0) REVERT: D 42 GLU cc_start: 0.7545 (tt0) cc_final: 0.7245 (tt0) outliers start: 23 outliers final: 18 residues processed: 134 average time/residue: 0.1941 time to fit residues: 35.4750 Evaluate side-chains 126 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 0.0570 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8042 Z= 0.254 Angle : 0.569 8.814 10953 Z= 0.303 Chirality : 0.044 0.219 1285 Planarity : 0.004 0.039 1392 Dihedral : 6.170 105.802 1152 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.55 % Allowed : 18.60 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.26), residues: 1042 helix: 2.43 (0.27), residues: 356 sheet: 0.33 (0.32), residues: 270 loop : -1.38 (0.26), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 151 HIS 0.004 0.001 HIS E 220 PHE 0.017 0.002 PHE E 80 TYR 0.012 0.001 TYR A 174 ARG 0.003 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 106 time to evaluate : 0.950 Fit side-chains REVERT: A 318 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6114 (mt-10) REVERT: A 343 ASN cc_start: 0.6789 (t0) cc_final: 0.6549 (t0) REVERT: B 73 LYS cc_start: 0.8376 (ttpt) cc_final: 0.7989 (tmtt) REVERT: B 126 LYS cc_start: 0.8727 (tttt) cc_final: 0.8478 (ttpt) REVERT: B 164 PHE cc_start: 0.7414 (m-80) cc_final: 0.7116 (m-80) REVERT: B 166 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6219 (tm-30) REVERT: B 195 LYS cc_start: 0.8788 (tmmt) cc_final: 0.8388 (tppt) REVERT: D 42 GLU cc_start: 0.7664 (tt0) cc_final: 0.7383 (tt0) REVERT: E 82 GLN cc_start: 0.7553 (tp40) cc_final: 0.7348 (tp40) outliers start: 35 outliers final: 25 residues processed: 128 average time/residue: 0.1834 time to fit residues: 32.9204 Evaluate side-chains 127 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.0010 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 85 optimal weight: 9.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8042 Z= 0.128 Angle : 0.479 7.438 10953 Z= 0.254 Chirality : 0.042 0.272 1285 Planarity : 0.003 0.033 1392 Dihedral : 5.823 100.895 1152 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.25 % Allowed : 20.03 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 1042 helix: 2.78 (0.27), residues: 356 sheet: 0.37 (0.31), residues: 282 loop : -1.25 (0.26), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 151 HIS 0.002 0.001 HIS E 35 PHE 0.011 0.001 PHE C 199 TYR 0.008 0.001 TYR A 174 ARG 0.001 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 0.895 Fit side-chains REVERT: A 179 ASN cc_start: 0.8033 (p0) cc_final: 0.7537 (p0) REVERT: A 318 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5847 (mt-10) REVERT: A 343 ASN cc_start: 0.6642 (t0) cc_final: 0.6398 (t0) REVERT: B 73 LYS cc_start: 0.8297 (ttpt) cc_final: 0.7899 (tmtt) REVERT: B 77 ASP cc_start: 0.7240 (t0) cc_final: 0.6981 (t0) REVERT: B 122 LEU cc_start: 0.8409 (mt) cc_final: 0.8200 (mt) REVERT: B 126 LYS cc_start: 0.8676 (tttt) cc_final: 0.8411 (ttpt) REVERT: B 164 PHE cc_start: 0.7381 (m-80) cc_final: 0.7150 (m-80) REVERT: B 166 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6317 (tm-30) REVERT: B 195 LYS cc_start: 0.8660 (tmmt) cc_final: 0.8395 (tppt) REVERT: C 186 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8284 (m-30) REVERT: C 268 ASN cc_start: 0.6482 (m110) cc_final: 0.5963 (t0) REVERT: D 42 GLU cc_start: 0.7594 (tt0) cc_final: 0.7343 (tt0) outliers start: 25 outliers final: 19 residues processed: 126 average time/residue: 0.1846 time to fit residues: 32.1871 Evaluate side-chains 126 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8042 Z= 0.335 Angle : 0.605 9.882 10953 Z= 0.323 Chirality : 0.046 0.257 1285 Planarity : 0.004 0.040 1392 Dihedral : 6.394 102.485 1152 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.81 % Allowed : 19.90 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1042 helix: 2.44 (0.27), residues: 355 sheet: 0.38 (0.32), residues: 278 loop : -1.45 (0.26), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 151 HIS 0.005 0.001 HIS E 220 PHE 0.016 0.002 PHE C 199 TYR 0.021 0.002 TYR B 115 ARG 0.005 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 100 time to evaluate : 0.841 Fit side-chains REVERT: A 318 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6279 (mt-10) REVERT: A 343 ASN cc_start: 0.6855 (t0) cc_final: 0.6622 (t0) REVERT: B 8 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.5825 (mp0) REVERT: B 73 LYS cc_start: 0.8325 (ttpt) cc_final: 0.7959 (tmtt) REVERT: B 126 LYS cc_start: 0.8801 (tttt) cc_final: 0.8480 (ttpt) REVERT: B 164 PHE cc_start: 0.7312 (m-80) cc_final: 0.7032 (m-80) REVERT: B 166 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6272 (tm-30) REVERT: D 42 GLU cc_start: 0.7641 (tt0) cc_final: 0.7437 (tt0) outliers start: 37 outliers final: 26 residues processed: 125 average time/residue: 0.1792 time to fit residues: 31.0386 Evaluate side-chains 123 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8042 Z= 0.172 Angle : 0.500 7.607 10953 Z= 0.267 Chirality : 0.043 0.281 1285 Planarity : 0.003 0.034 1392 Dihedral : 5.755 94.214 1152 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.64 % Allowed : 21.07 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.26), residues: 1042 helix: 2.63 (0.27), residues: 357 sheet: 0.31 (0.32), residues: 275 loop : -1.41 (0.26), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 151 HIS 0.003 0.001 HIS E 220 PHE 0.013 0.001 PHE C 199 TYR 0.015 0.001 TYR B 115 ARG 0.006 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 0.810 Fit side-chains REVERT: A 179 ASN cc_start: 0.8070 (p0) cc_final: 0.7549 (p0) REVERT: A 318 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.5977 (mt-10) REVERT: A 343 ASN cc_start: 0.6772 (t0) cc_final: 0.6486 (t0) REVERT: B 73 LYS cc_start: 0.8326 (ttpt) cc_final: 0.7916 (tmtt) REVERT: B 126 LYS cc_start: 0.8759 (tttt) cc_final: 0.8443 (ttpt) REVERT: B 164 PHE cc_start: 0.7257 (m-80) cc_final: 0.6981 (m-80) REVERT: B 166 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6286 (tm-30) REVERT: B 242 GLU cc_start: 0.7241 (tt0) cc_final: 0.7020 (tt0) REVERT: D 42 GLU cc_start: 0.7618 (tt0) cc_final: 0.7402 (tt0) outliers start: 28 outliers final: 22 residues processed: 119 average time/residue: 0.1680 time to fit residues: 28.4995 Evaluate side-chains 121 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8042 Z= 0.216 Angle : 0.528 8.568 10953 Z= 0.281 Chirality : 0.044 0.261 1285 Planarity : 0.003 0.033 1392 Dihedral : 5.728 95.393 1152 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.42 % Allowed : 20.55 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1042 helix: 2.58 (0.27), residues: 356 sheet: 0.31 (0.31), residues: 277 loop : -1.44 (0.26), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 151 HIS 0.004 0.001 HIS E 220 PHE 0.013 0.001 PHE C 199 TYR 0.021 0.001 TYR B 115 ARG 0.005 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 99 time to evaluate : 0.909 Fit side-chains REVERT: A 179 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7538 (p0) REVERT: A 318 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6067 (mt-10) REVERT: A 343 ASN cc_start: 0.6800 (t0) cc_final: 0.6512 (t0) REVERT: B 8 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.5745 (mp0) REVERT: B 73 LYS cc_start: 0.8320 (ttpt) cc_final: 0.7902 (tmtt) REVERT: B 126 LYS cc_start: 0.8767 (tttt) cc_final: 0.8459 (ttpt) REVERT: B 164 PHE cc_start: 0.7328 (m-80) cc_final: 0.7037 (m-80) REVERT: B 166 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6517 (tm-30) REVERT: B 242 GLU cc_start: 0.7287 (tt0) cc_final: 0.7071 (tt0) REVERT: C 153 ASP cc_start: 0.7017 (m-30) cc_final: 0.6806 (m-30) REVERT: D 42 GLU cc_start: 0.7635 (tt0) cc_final: 0.7420 (tt0) outliers start: 34 outliers final: 25 residues processed: 121 average time/residue: 0.1714 time to fit residues: 29.5024 Evaluate side-chains 126 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8042 Z= 0.169 Angle : 0.496 7.464 10953 Z= 0.263 Chirality : 0.043 0.272 1285 Planarity : 0.003 0.029 1392 Dihedral : 5.529 94.588 1152 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.77 % Allowed : 21.33 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1042 helix: 2.69 (0.27), residues: 357 sheet: 0.23 (0.31), residues: 280 loop : -1.38 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 151 HIS 0.003 0.001 HIS E 220 PHE 0.012 0.001 PHE C 199 TYR 0.019 0.001 TYR B 115 ARG 0.006 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 101 time to evaluate : 0.849 Fit side-chains REVERT: A 179 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7434 (p0) REVERT: A 318 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.5894 (mt-10) REVERT: A 343 ASN cc_start: 0.6709 (t0) cc_final: 0.6431 (t0) REVERT: B 73 LYS cc_start: 0.8327 (ttpt) cc_final: 0.7902 (tmtt) REVERT: B 126 LYS cc_start: 0.8749 (tttt) cc_final: 0.8470 (ttpt) REVERT: B 164 PHE cc_start: 0.7283 (m-80) cc_final: 0.7018 (m-80) REVERT: B 166 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6521 (tm-30) REVERT: B 242 GLU cc_start: 0.7271 (tt0) cc_final: 0.7023 (tt0) REVERT: C 153 ASP cc_start: 0.7021 (m-30) cc_final: 0.6803 (m-30) REVERT: C 268 ASN cc_start: 0.6659 (m110) cc_final: 0.6154 (t0) REVERT: D 42 GLU cc_start: 0.7622 (tt0) cc_final: 0.7389 (tt0) REVERT: E 232 LYS cc_start: 0.8603 (tttp) cc_final: 0.8387 (tttm) outliers start: 29 outliers final: 26 residues processed: 119 average time/residue: 0.1767 time to fit residues: 29.5303 Evaluate side-chains 125 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 96 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 74 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8042 Z= 0.205 Angle : 0.520 8.319 10953 Z= 0.276 Chirality : 0.043 0.273 1285 Planarity : 0.003 0.031 1392 Dihedral : 5.560 95.642 1151 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.90 % Allowed : 21.07 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1042 helix: 2.61 (0.27), residues: 357 sheet: 0.28 (0.31), residues: 282 loop : -1.39 (0.26), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 151 HIS 0.003 0.001 HIS E 220 PHE 0.013 0.001 PHE C 199 TYR 0.019 0.001 TYR B 115 ARG 0.004 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 97 time to evaluate : 0.836 Fit side-chains REVERT: A 179 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7464 (p0) REVERT: A 318 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.5993 (mt-10) REVERT: A 343 ASN cc_start: 0.6749 (t0) cc_final: 0.6468 (t0) REVERT: B 8 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.5716 (mp0) REVERT: B 73 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7895 (tmtt) REVERT: B 126 LYS cc_start: 0.8774 (tttt) cc_final: 0.8473 (ttpt) REVERT: B 164 PHE cc_start: 0.7320 (m-80) cc_final: 0.7039 (m-80) REVERT: B 166 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6524 (tm-30) REVERT: B 242 GLU cc_start: 0.7321 (tt0) cc_final: 0.7098 (tt0) REVERT: C 153 ASP cc_start: 0.7048 (m-30) cc_final: 0.6827 (m-30) REVERT: C 268 ASN cc_start: 0.6678 (m110) cc_final: 0.6174 (t0) REVERT: D 42 GLU cc_start: 0.7655 (tt0) cc_final: 0.7427 (tt0) outliers start: 30 outliers final: 24 residues processed: 116 average time/residue: 0.1557 time to fit residues: 26.2647 Evaluate side-chains 123 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8042 Z= 0.319 Angle : 0.604 9.933 10953 Z= 0.322 Chirality : 0.046 0.300 1285 Planarity : 0.004 0.034 1392 Dihedral : 5.934 99.928 1151 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.29 % Allowed : 20.94 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1042 helix: 2.28 (0.27), residues: 355 sheet: 0.18 (0.31), residues: 283 loop : -1.48 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 151 HIS 0.004 0.001 HIS E 220 PHE 0.016 0.002 PHE C 199 TYR 0.021 0.002 TYR B 115 ARG 0.005 0.001 ARG B 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 99 time to evaluate : 0.964 Fit side-chains REVERT: A 179 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7647 (p0) REVERT: A 228 LEU cc_start: 0.6268 (mt) cc_final: 0.6058 (pp) REVERT: A 318 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6353 (mt-10) REVERT: A 343 ASN cc_start: 0.6784 (t0) cc_final: 0.6524 (t0) REVERT: B 8 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6013 (mp0) REVERT: B 73 LYS cc_start: 0.8343 (ttpt) cc_final: 0.7908 (tmtt) REVERT: B 126 LYS cc_start: 0.8842 (tttt) cc_final: 0.8524 (ttpt) REVERT: B 164 PHE cc_start: 0.7245 (m-80) cc_final: 0.6990 (m-80) REVERT: B 166 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6488 (tm-30) REVERT: C 153 ASP cc_start: 0.7062 (m-30) cc_final: 0.6859 (m-30) REVERT: C 268 ASN cc_start: 0.6907 (m110) cc_final: 0.6287 (t0) REVERT: E 232 LYS cc_start: 0.8588 (tttp) cc_final: 0.8382 (tttm) outliers start: 33 outliers final: 26 residues processed: 123 average time/residue: 0.1824 time to fit residues: 31.4532 Evaluate side-chains 126 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 96 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.128890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103385 restraints weight = 11099.233| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.94 r_work: 0.2977 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8042 Z= 0.367 Angle : 0.643 10.392 10953 Z= 0.343 Chirality : 0.047 0.311 1285 Planarity : 0.004 0.034 1392 Dihedral : 6.159 103.243 1151 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.42 % Allowed : 20.94 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1042 helix: 1.98 (0.27), residues: 355 sheet: 0.15 (0.31), residues: 279 loop : -1.59 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 151 HIS 0.005 0.001 HIS E 220 PHE 0.018 0.002 PHE C 199 TYR 0.024 0.002 TYR B 115 ARG 0.005 0.001 ARG D 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1797.55 seconds wall clock time: 33 minutes 10.78 seconds (1990.78 seconds total)